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"type": "string" }, "confidence": { "type": "integer" }, "end": { "type": "integer" }, "historic": { "type": "boolean" }, "id": { "type": "string" }, "negated": { "type": "boolean" }, "uncertain": { "type": "boolean" } } } }, "name": { "type": "string" }, "relations": { "type": "array", "items": { "type": "object", "properties": { "sourceId": { "type": "string" }, "targetId": { "type": "string" }, "type": { "type": "string" } } } }, "sections": { "type": "array", "items": { "type": "object", "properties": { "begin": { "type": "integer" }, "end": { "type": "integer" }, "id": { "type": "string" }, "type": { "type": "string" } } } }, "text": { "type": "string" }, "type": { "type": "string" } } } } } }, "PatientDiagnosis": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "classUri": { "type": "string" }, "patientId": { "type": "string" } } }, "PatientInfo": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "birthDate": { "type": "string" }, "firstEncounterAge": { "type": "string" }, "firstEncounterDate": { "type": "string" }, "gender": { "type": "string" }, "lastEncounterAge": { "type": "string" }, "lastEncounterDate": { "type": "string" }, "patientId": { "type": "string" }, "patientName": { "type": "string" } } }, "PatientInfoAndStages": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "birthDate": { "type": "string" }, "firstEncounterAge": { "type": "string" }, "firstEncounterDate": { "type": "string" }, "gender": { "type": "string" }, "lastEncounterAge": { "type": "string" }, "lastEncounterDate": { "type": "string" }, "patientId": { "type": "string" }, "patientName": { "type": "string" }, "stages": { "type": "array", "items": { "type": "string" } } } }, "PatientSummary": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "id": { "type": "string" }, "neoplasms": { "type": "array", "items": { "$ref": "#/components/schemas/NeoplasmSummary" } }, "patient": { "type": "object", "properties": { "biomarkers": { "type": "array", "items": { "type": "object", "properties": { "patientId": { "type": "string" }, "relationPrettyName": { "type": "string" }, "tumorFactRelation": { "type": "string" }, "valueText": { "type": "string" } } } }, "birth": { "type": "string" }, "death": { "type": "string" }, "diagnoses": { "type": "array", "items": { "type": "object", "properties": { "diagnosis": { "type": "array", "items": { "type": "string" } }, "diagnosisGroups": { "type": "array", "items": { "type": "string" } }, "patientId": { "type": "string" } } } }, "gender": { "type": "string" }, "id": { "type": "string" }, "name": { "type": "string" }, "noteHash": { "type": "string" }, "notes": { "type": "array", "items": { "type": "object", "properties": { "corefs": { "type": "array", "items": { "type": "object", "properties": { "id": { "type": "string" }, "idChain": { "type": "array", "items": { "type": "string" } } } } }, "date": { "type": "string" }, "episode": { "type": "string" }, "id": { "type": "string" }, "mentions": { "type": "array", "items": { "$ref": "#/components/schemas/Mention" } }, "name": { "type": "string" }, "relations": { "type": "array", "items": { "type": "object", "properties": { "sourceId": { "type": "string" }, "targetId": { "type": "string" }, "type": { "type": "string" } } } }, "sections": { "type": "array", "items": { "type": "object", "properties": { "begin": { "type": "integer" }, "end": { "type": "integer" }, "id": { "type": "string" }, "type": { "type": "string" } } } }, "text": { "type": "string" }, "type": { "type": "string" } } } } } } } }, "PatientSummaryAndStagesList": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "patientSummaryAndStages": { "type": "array", "items": { "type": "object", "properties": { "birthDate": { "type": "string" }, "firstEncounterAge": { "type": "string" }, "firstEncounterDate": { "type": "string" }, "gender": { "type": "string" }, "lastEncounterAge": { "type": "string" }, "lastEncounterDate": { "type": "string" }, "patientId": { "type": "string" }, "patientName": { "type": "string" }, "stages": { "type": "array", "items": { "type": "string" } } } } } } }, "PatientSummaryXn": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "birth": { "type": "string" }, "cancers": { "type": "array", "items": { "type": "object", "properties": { "attributes": { "type": "array", "items": { "$ref": "#/components/schemas/AttributeXn" } }, "classUri": { "type": "string" }, "conceptIds": { "type": "array", "items": { "type": "string" } }, "confidence": { "type": "integer" }, "historic": { "type": "boolean" }, "id": { "type": "string" }, "negated": { "type": "boolean" }, "tumors": { "type": "array", "items": { "type": "object", "properties": { "attributes": { "type": "array", "items": { "$ref": "#/components/schemas/AttributeXn" } }, "classUri": { "type": "string" }, "conceptIds": { "type": "array", "items": { "type": "string" } }, "confidence": { "type": "integer" }, "historic": { "type": "boolean" }, "id": { "type": "string" }, "negated": { "type": "boolean" }, "uncertain": { "type": "boolean" } } } }, "uncertain": { "type": "boolean" } } } }, "conceptRelations": { "type": "array", "items": { "type": "object", "properties": { "sourceId": { "type": "string" }, "targetId": { "type": "string" }, "type": { "type": "string" } } } }, "concepts": { "type": "array", "items": { "type": "object", "properties": { "classUri": { "type": "string" }, "codifications": { "type": "array", "items": { "type": "object", "properties": { "codes": { "type": "array", "items": { "type": "string" } }, "source": { "type": "string" } } } }, "confidence": { "type": "integer" }, "dpheGroup": { "type": "string" }, "historic": { "type": "boolean" }, "id": { "type": "string" }, "mentionIds": { "type": "array", "items": { "type": "string" } }, "negated": { "type": "boolean" }, "preferredText": { "type": "string" }, "uncertain": { "type": "boolean" } } } }, "death": { "type": "string" }, "documents": { "type": "array", "items": { "type": "object", "properties": { "date": { "type": "string" }, "episode": { "type": "string" }, "id": { "type": "string" }, "mentionRelations": { "type": "array", "items": { "type": "object", "properties": { "sourceId": { "type": "string" }, "targetId": { "type": "string" }, "type": { "type": "string" } } } }, "mentions": { "type": "array", "items": { "type": "object", "properties": { "begin": { "type": "integer" }, "classUri": { "type": "string" }, "confidence": { "type": "integer" }, "end": { "type": "integer" }, "historic": { "type": "boolean" }, "id": { "type": "string" }, "negated": { "type": "boolean" }, "uncertain": { "type": "boolean" } } } }, "name": { "type": "string" }, "sections": { "type": "array", "items": { "type": "object", "properties": { "begin": { "type": "integer" }, "end": { "type": "integer" }, "id": { "type": "string" }, "type": { "type": "string" } } } }, "text": { "type": "string" }, "type": { "type": "string" } } } }, "gender": { "type": "string" }, "id": { "type": "string" }, "name": { "type": "string" } } }, "PatientXn": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "biomarkers": { "type": "array", "items": { "type": "object", "properties": { "patientId": { "type": "string" }, "relationPrettyName": { "type": "string" }, "tumorFactRelation": { "type": "string" }, "valueText": { "type": "string" } } } }, "birth": { "type": "string" }, "death": { "type": "string" }, "diagnoses": { "type": "array", "items": { "type": "object", "properties": { "diagnosis": { "type": "array", "items": { "type": "string" } }, "diagnosisGroups": { "type": "array", "items": { "type": "string" } }, "patientId": { "type": "string" } } } }, "gender": { "type": "string" }, "id": { "type": "string" }, "name": { "type": "string" }, "noteHash": { "type": "string" }, "notes": { "type": "array", "items": { "type": "object", "properties": { "corefs": { "type": "array", "items": { "type": "object", "properties": { "id": { "type": "string" }, "idChain": { "type": "array", "items": { "type": "string" } } } } }, "date": { "type": "string" }, "episode": { "type": "string" }, "id": { "type": "string" }, "mentions": { "type": "array", "items": { "type": "object", "properties": { "begin": { "type": "integer" }, "classUri": { "type": "string" }, "confidence": { "type": "integer" }, "end": { "type": "integer" }, "historic": { "type": "boolean" }, "id": { "type": "string" }, "negated": { "type": "boolean" }, "uncertain": { "type": "boolean" } } } }, "name": { "type": "string" }, "relations": { "type": "array", "items": { "type": "object", "properties": { "sourceId": { "type": "string" }, "targetId": { "type": "string" }, "type": { "type": "string" } } } }, "sections": { "type": "array", "items": { "type": "object", "properties": { "begin": { "type": "integer" }, "end": { "type": "integer" }, "id": { "type": "string" }, "type": { "type": "string" } } } }, "text": { "type": "string" }, "type": { "type": "string" } } } } } }, "Report": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "reportDate": { "type": "string" }, "reportEpisode": { "type": "string" }, "reportId": { "type": "string" }, "reportType": { "type": "string" } } }, "Section": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "begin": { "type": "integer" }, "end": { "type": "integer" }, "id": { "type": "string" }, "type": { "type": "string" } } }, "SharedPatientProperties": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object" }, "Text": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "name": { "type": "string" }, "value": { "type": "string" } } }, "Tumor": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "attributes": { "type": "array", "items": { "type": "object", "properties": { "classUri": { "type": "string" }, "confidence": { "type": "integer" }, "confidenceFeatures": { "type": "array", "items": { "type": "integer" } }, "directEvidence": { "type": "array", "items": { "$ref": "#/components/schemas/Mention" } }, "id": { "type": "string" }, "indirectEvidence": { "type": "array", "items": { "$ref": "#/components/schemas/Mention" } }, "name": { "type": "string" }, "notEvidence": { "type": "array", "items": { "$ref": "#/components/schemas/Mention" } }, "value": { "type": "string" } } } }, "classUri": { "type": "string" }, "factIds": { "type": "array", "items": { "type": "string" } }, "id": { "type": "string" }, "relatedFactIds": { "type": "object" } } }, "TumorFact": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "relation": { "type": "string" }, "relationPrettyName": { "type": "string" }, "tumorFactInfo": { "type": "object", "properties": { "id": { "type": "string" }, "name": { "type": "string" }, "prettyName": { "type": "string" } } } } }, "TumorSummary": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "hasTumorType": { "type": "string" }, "tumorFacts": { "type": "array", "items": { "type": "object", "properties": { "relation": { "type": "string" }, "relationPrettyName": { "type": "string" }, "tumorFactInfo": { "type": "object", "properties": { "id": { "type": "string" }, "name": { "type": "string" }, "prettyName": { "type": "string" } } } } } }, "tumorId": { "type": "string" } } }, "TumorSummaryXn": { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "attributes": { "type": "array", "items": { "type": "object", "properties": { "id": { "type": "string" }, "name": { "type": "string" }, "values": { "type": "array", "items": { "type": "object", "properties": { "classUri": { "type": "string" }, "conceptIds": { "type": "array", "items": { "type": "string" } }, "confidence": { "type": "integer" }, "historic": { "type": "boolean" }, "id": { "type": "string" }, "negated": { "type": "boolean" }, "uncertain": { "type": "boolean" }, "value": { "type": "string" } } } } } } }, "classUri": { "type": "string" }, "conceptIds": { "type": "array", "items": { "type": "string" } }, "confidence": { "type": "integer" }, "historic": { "type": "boolean" }, "id": { "type": "string" }, "negated": { "type": "boolean" }, "uncertain": { "type": "boolean" } } } } }, "paths": { "/v1/deepphe-api/deepphe/attributes/classes": { "get": { "summary": "Get all unique attribute classes", "description": "Returns list of unique attribute class names", "tags": [ "DeepPhe" ], "responses": { "200": { "description": "List of attribute class names", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "string" } } } } }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/attributes/summary": { "get": { "summary": "Get all attribute classes and instances in one response", "description": "Returns attribute classes with instances grouped by class, with optional patient identifier data", "tags": [ "DeepPhe" ], "parameters": [ { "in": "query", "name": "includePatientIds", "schema": { "type": "boolean", "default": true }, "required": false, "description": "When false, omit patient identifier arrays from instance rows" } ], "responses": { "200": { "description": "Attribute summary payload", "content": { "application/json": { "schema": { "type": "object", "properties": { "classes": { "type": "array", "items": { "type": "string" } }, "instancesByClass": { "type": "object", "additionalProperties": { "type": "array", "items": { "type": "object" } } }, "timing": { "type": "object", "properties": { "totalMs": { "type": "number" } } } } } } } }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/attributes/instances": { "get": { "summary": "Get all attribute instances for a specific class", "description": "Returns list of attribute objects for a specific class (without patient identifier arrays)", "tags": [ "DeepPhe" ], "parameters": [ { "in": "query", "name": "groupname", "schema": { "type": "string" }, "required": true, "description": "Group name" } ], "responses": { "200": { "description": "List of attributes", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "object", "properties": { "id": { "type": "integer", "description": "Unique identifier for the attribute" }, "attribute_name": { "type": "string", "description": "Name of the attribute class" }, "value": { "type": "string", "description": "Value of the attribute" }, "classUri": { "type": "string", "description": "URI of the class" }, "negated": { "type": "integer", "description": "Flag indicating if the attribute is negated (0 or 1)" }, "uncertain": { "type": "integer", "description": "Flag indicating if the attribute is uncertain (0 or 1)" }, "historic": { "type": "integer", "description": "Flag indicating if the attribute is historic (0 or 1)" }, "num_patients": { "type": "integer", "description": "Number of patients with this attribute" } } }, "example": [ { "id": 894, "attribute_name": "Genes", "value": "Cyclin-Dependent Kinase Inhibitor 2A", "classUri": "Cyclin_sub_DependentKinaseInhibitor2A", "negated": 0, "uncertain": 1, "historic": 0, "num_patients": 1 } ] } } } }, "400": { "description": "Missing required parameters" }, "404": { "description": "No attributes found for this class" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/attributes/instances/patients": { "get": { "summary": "Get all attribute instances for a specific class including patient identifiers", "description": "Returns list of attribute objects for a specific class with patient identifier arrays", "tags": [ "DeepPhe" ], "parameters": [ { "in": "query", "name": "groupname", "schema": { "type": "string" }, "required": true, "description": "Group name" } ], "responses": { "200": { "description": "List of attributes with patient identifier arrays" }, "400": { "description": "Missing required parameters" }, "404": { "description": "No attributes found for this class" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/attributes/instances/patient/{patientId}": { "get": { "summary": "Get attribute instances for a specific class and patient", "description": "Returns attribute rows where the specified patient appears", "tags": [ "DeepPhe" ], "parameters": [ { "in": "path", "name": "patientId", "schema": { "type": "string" }, "required": true, "description": "Patient ID" }, { "in": "query", "name": "groupname", "schema": { "type": "string" }, "required": true, "description": "Group name" } ], "responses": { "200": { "description": "List of matching attributes" }, "400": { "description": "Missing required parameters" }, "404": { "description": "No attributes found for this class and patient" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/cancers/classes": { "get": { "summary": "Get all unique cancer classes", "description": "Returns list of unique cancer class classUri values", "tags": [ "DeepPhe" ], "responses": { "200": { "description": "List of cancer class classUri values", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "string" } } } } }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/cancers/summary": { "get": { "summary": "Get all cancer classes and instances in one response", "description": "Returns cancer classes with instances grouped by class, with optional patient identifier data", "tags": [ "DeepPhe" ], "parameters": [ { "in": "query", "name": "includePatientIds", "schema": { "type": "boolean", "default": true }, "required": false, "description": "When false, omit patient identifier arrays from instance rows" } ], "responses": { "200": { "description": "Cancer summary payload", "content": { "application/json": { "schema": { "type": "object", "properties": { "classes": { "type": "array", "items": { "type": "string" } }, "instancesByClass": { "type": "object", "additionalProperties": { "type": "array", "items": { "type": "object" } } }, "timing": { "type": "object", "properties": { "totalMs": { "type": "number" } } } } } } } }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/cancers/instances": { "get": { "summary": "Get all cancer instances for a specific class", "description": "Returns list of cancer objects for a specific class (without patient identifier arrays)", "tags": [ "DeepPhe" ], "parameters": [ { "in": "query", "name": "classUri", "schema": { "type": "string" }, "required": true, "description": "Class URI" } ], "responses": { "200": { "description": "List of cancers", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "object", "properties": { "id": { "type": "integer", "description": "Unique identifier for the cancer" }, "classUri": { "type": "string", "description": "URI of the cancer class" }, "value": { "type": "string", "description": "Value of the cancer" }, "negated": { "type": "integer", "description": "Flag indicating if the cancer is negated (0 or 1)" }, "uncertain": { "type": "integer", "description": "Flag indicating if the cancer is uncertain (0 or 1)" }, "historic": { "type": "integer", "description": "Flag indicating if the cancer is historic (0 or 1)" }, "num_patients": { "type": "integer", "description": "Number of patients with this cancer" } } }, "example": [ { "id": 123, "classUri": "Breast_Cancer", "value": "Breast Cancer", "negated": 0, "uncertain": 0, "historic": 0, "num_patients": 5 } ] } } } }, "400": { "description": "Missing required parameters" }, "404": { "description": "No cancers found for this class" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/cancers/instances/patients": { "get": { "summary": "Get all cancer instances for a specific class including patient identifiers", "description": "Returns list of cancer objects for a specific class with patient identifier arrays", "tags": [ "DeepPhe" ], "parameters": [ { "in": "query", "name": "classUri", "schema": { "type": "string" }, "required": true, "description": "Class URI" } ], "responses": { "200": { "description": "List of cancers with patient identifier arrays" }, "400": { "description": "Missing required parameters" }, "404": { "description": "No cancers found for this class" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/cancers/instances/patient/{patientId}": { "get": { "summary": "Get cancer instances for a specific class and patient", "description": "Returns cancer rows where the specified patient appears", "tags": [ "DeepPhe" ], "parameters": [ { "in": "path", "name": "patientId", "schema": { "type": "string" }, "required": true, "description": "Patient ID" }, { "in": "query", "name": "classUri", "schema": { "type": "string" }, "required": true, "description": "Class URI" } ], "responses": { "200": { "description": "List of matching cancers" }, "400": { "description": "Missing required parameters" }, "404": { "description": "No cancers found for this class and patient" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/concepts/classes": { "get": { "summary": "Get all unique concept classes", "description": "Returns list of unique concept class dpheGroup values", "tags": [ "DeepPhe" ], "responses": { "200": { "description": "List of concept class dpheGroup values", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "string" } } } } }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/concepts/summary": { "get": { "summary": "Get all concept classes and instances in one response", "description": "Returns concept classes with instances grouped by class, with optional patient identifier data", "tags": [ "DeepPhe" ], "parameters": [ { "in": "query", "name": "includePatientIds", "schema": { "type": "boolean", "default": true }, "required": false, "description": "When false, omit patient identifier arrays from instance rows" } ], "responses": { "200": { "description": "Concept summary payload", "content": { "application/json": { "schema": { "type": "object", "properties": { "classes": { "type": "array", "items": { "type": "string" } }, "instancesByClass": { "type": "object", "additionalProperties": { "type": "array", "items": { "type": "object" } } }, "timing": { "type": "object", "properties": { "totalMs": { "type": "number" } } } } } } } }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/concepts/instances": { "get": { "summary": "Get all concept instances for a specific class", "description": "Returns list of concept objects for a specific class (without patient identifier arrays)", "tags": [ "DeepPhe" ], "parameters": [ { "in": "query", "name": "dpheGroup", "schema": { "type": "string" }, "required": true, "description": "DPHE Group" } ], "responses": { "200": { "description": "List of concepts", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "object", "properties": { "id": { "type": "integer", "description": "Unique identifier for the concept" }, "dpheGroup": { "type": "string", "description": "DPHE Group of the concept" }, "value": { "type": "string", "description": "Value of the concept" }, "classUri": { "type": "string", "description": "URI of the concept class" }, "negated": { "type": "integer", "description": "Flag indicating if the concept is negated (0 or 1)" }, "uncertain": { "type": "integer", "description": "Flag indicating if the concept is uncertain (0 or 1)" }, "historic": { "type": "integer", "description": "Flag indicating if the concept is historic (0 or 1)" }, "num_patients": { "type": "integer", "description": "Number of patients with this concept" } } }, "example": [ { "id": 456, "dpheGroup": "Biomarkers", "value": "HER2", "classUri": "HER2_Biomarker", "negated": 0, "uncertain": 0, "historic": 0, "num_patients": 3 } ] } } } }, "400": { "description": "Missing required parameters" }, "404": { "description": "No concepts found for this class" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/concepts/instances/patients": { "get": { "summary": "Get all concept instances for a specific class including patient identifiers", "description": "Returns list of concept objects for a specific class with patient identifier arrays", "tags": [ "DeepPhe" ], "parameters": [ { "in": "query", "name": "dpheGroup", "schema": { "type": "string" }, "required": true, "description": "DPHE Group" } ], "responses": { "200": { "description": "List of concepts with patient identifier arrays" }, "400": { "description": "Missing required parameters" }, "404": { "description": "No concepts found for this class" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/concepts/instances/patient/{patientId}": { "get": { "summary": "Get concept instances for a specific class and patient", "description": "Returns concept rows where the specified patient appears", "tags": [ "DeepPhe" ], "parameters": [ { "in": "path", "name": "patientId", "schema": { "type": "string" }, "required": true, "description": "Patient ID" }, { "in": "query", "name": "dpheGroup", "schema": { "type": "string" }, "required": true, "description": "DPHE Group" } ], "responses": { "200": { "description": "List of matching concepts" }, "400": { "description": "Missing required parameters" }, "404": { "description": "No concepts found for this class and patient" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/filter/count": { "post": { "summary": "Count patients matching multi-criteria filters", "description": "Accepts an array of filter items. Each item specifies a data type\n(omop, attributes, cancers, concepts), a class within that type,\nand one or more instance values.\n\n**Within** an item the instances are OR'd: a patient matches if they\nhave *any* of the listed values.\n\n**Across** items the results are AND'd: a patient must satisfy\n*every* filter item.\n\nTiming metrics are always returned so callers can monitor performance.\n", "tags": [ "Filter" ], "parameters": [ { "in": "query", "name": "includePatientIds", "schema": { "type": "boolean", "default": false }, "description": "When true, also return the list of matching patient IDs" }, { "in": "query", "name": "autoIncludeThreshold", "schema": { "type": "integer", "default": 20 }, "description": "Automatically include patient IDs when the matching count is\nbelow this threshold, even when includePatientIds is false.\nSet to 0 to disable auto-inclusion.\n" } ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "type": "object", "required": [ "filters" ], "properties": { "filters": { "type": "array", "minItems": 1, "items": { "type": "object", "required": [ "type", "class", "instances" ], "properties": { "type": { "type": "string", "enum": [ "omop", "attributes", "cancers", "concepts" ] }, "class": { "type": "string" }, "instances": { "type": "array", "minItems": 1, "items": { "type": "string" } } } } } } }, "example": { "filters": [ { "type": "omop", "class": "RACE", "instances": [ "White", "Black" ] }, { "type": "omop", "class": "CANCER", "instances": [ "B" ] }, { "type": "attributes", "class": "Behavior", "instances": [ "Benign", "Invasive" ] } ] } } } }, "responses": { "200": { "description": "Patient count with timing metrics", "content": { "application/json": { "schema": { "type": "object", "properties": { "count": { "type": "integer" }, "patient_ids": { "type": "array", "items": { "type": "string" } }, "timing": { "type": "object", "properties": { "queryMs": { "type": "number" }, "bitmapMs": { "type": "number" }, "resolveMs": { "type": "number" }, "totalMs": { "type": "number" }, "itemCounts": { "type": "array", "items": { "type": "integer" } } } } } } } } }, "400": { "description": "Validation error" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/filter/count/batch": { "post": { "summary": "Batch count patients for multiple independent filter queries", "description": "Accepts an array of independent filter queries and returns a result for\neach in positional order. All queries are executed concurrently on the\nserver, replacing N sequential HTTP round trips with a single request.\n\nEach query uses the same filter schema as POST /count. Per-query errors\nare captured and returned inline rather than failing the entire batch.\n", "tags": [ "Filter" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "type": "object", "required": [ "queries" ], "properties": { "queries": { "type": "array", "minItems": 1, "maxItems": 500, "items": { "type": "object", "required": [ "filters" ], "properties": { "filters": { "type": "array", "minItems": 1, "items": { "type": "object", "required": [ "type", "class", "instances" ], "properties": { "type": { "type": "string", "enum": [ "omop", "attributes", "cancers", "concepts" ] }, "class": { "type": "string" }, "instances": { "type": "array", "minItems": 1 } } } }, "includePatientIds": { "type": "boolean", "default": false }, "autoIncludeThreshold": { "type": "integer", "default": 20 } } } } } } } } }, "responses": { "200": { "description": "Array of per-query results in positional order", "content": { "application/json": { "schema": { "type": "object", "properties": { "results": { "type": "array", "items": { "type": "object", "properties": { "count": { "type": "integer" }, "patient_ids": { "type": "array", "items": { "type": "string" } }, "timing": { "type": "object" }, "error": { "type": "string", "description": "Present only when this individual query failed" } } } } } } } } }, "400": { "description": "Validation error" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/filter/summary": { "post": { "summary": "Get patient summaries for a list of patient IDs", "description": "Accepts a set of patient IDs and returns matching patient summaries\nfrom patient_summaries with uncompressed json_text payloads.\n", "tags": [ "Filter" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "type": "object", "required": [ "patient_ids" ], "properties": { "patient_ids": { "type": "array", "minItems": 1, "items": { "oneOf": [ { "type": "string" }, { "type": "number" } ] } } } } } } }, "responses": { "200": { "description": "List of patient summaries with uncompressed json_text", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "object", "properties": { "patient_id": { "type": "string" }, "json_text": { "type": "string" } } } } } } }, "400": { "description": "Validation error" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/omop/classes": { "get": { "summary": "Get all supported OMOP classes", "description": "Returns list of OMOP class names available for OMOP instances queries", "tags": [ "OMOP" ], "responses": { "200": { "description": "List of OMOP class names", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "string" } } } } }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/omop/summary": { "get": { "summary": "Get all OMOP classes and instances in one response", "description": "Returns OMOP classes with instances grouped by class, with optional patient identifier data", "tags": [ "OMOP" ], "parameters": [ { "in": "query", "name": "includePatientIds", "schema": { "type": "boolean", "default": true }, "required": false, "description": "When false, omit patient identifier arrays from instance rows" } ], "responses": { "200": { "description": "OMOP summary payload", "content": { "application/json": { "schema": { "type": "object", "properties": { "classes": { "type": "array", "items": { "type": "string" } }, "instancesByClass": { "type": "object", "additionalProperties": { "type": "array", "items": { "type": "object" } } }, "timing": { "type": "object", "properties": { "totalMs": { "type": "number" } } } } } } } }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/omop/instances": { "get": { "summary": "Get all OMOP instances for a specific class", "description": "Returns OMOP rows from one of the OMOP tables by class (without patient identifier arrays)", "tags": [ "OMOP" ], "parameters": [ { "in": "query", "name": "attribute", "schema": { "type": "string", "enum": [ "AGE_AT_DX", "ETHNICITY", "GENDER", "RACE", "CANCER" ] }, "required": true, "description": "OMOP class to retrieve" } ], "responses": { "200": { "description": "OMOP class rows", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "object" } } } } }, "400": { "description": "Missing or invalid required parameters" }, "404": { "description": "No OMOP rows found for this class" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/omop/instances/patients": { "get": { "summary": "Get all OMOP instances for a specific class including patient identifiers", "description": "Returns OMOP rows from one of the OMOP tables by class with patient identifier arrays", "tags": [ "OMOP" ], "parameters": [ { "in": "query", "name": "attribute", "schema": { "type": "string", "enum": [ "AGE_AT_DX", "ETHNICITY", "GENDER", "RACE", "CANCER" ] }, "required": true, "description": "OMOP class to retrieve" } ], "responses": { "200": { "description": "OMOP class rows with patient identifier arrays" }, "400": { "description": "Missing or invalid required parameters" }, "404": { "description": "No OMOP rows found for this class" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/omop/instances/patient/{patientId}": { "get": { "summary": "Get OMOP instances for a specific class and patient", "description": "Returns OMOP rows where the specified patient appears", "tags": [ "OMOP" ], "parameters": [ { "in": "path", "name": "patientId", "schema": { "type": "string" }, "required": true, "description": "Patient ID" }, { "in": "query", "name": "attribute", "schema": { "type": "string", "enum": [ "AGE_AT_DX", "ETHNICITY", "GENDER", "RACE", "CANCER" ] }, "required": true, "description": "OMOP class to retrieve" } ], "responses": { "200": { "description": "Matching OMOP class rows for the patient" }, "400": { "description": "Missing or invalid required parameters" }, "404": { "description": "No OMOP rows found for this class and patient" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/patient/{patientId}": { "get": { "summary": "Get patient documents with text excluded by default", "description": "Returns list of DocumentXn objects for a specific patient, with the text field excluded.", "tags": [ "DeepPhe" ], "parameters": [ { "in": "path", "name": "patientId", "schema": { "type": "string" }, "required": true, "description": "Patient ID" } ], "responses": { "200": { "description": "List of DocumentXn objects without text", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/DocumentXn" } } } } }, "400": { "description": "Missing or invalid patientId" }, "404": { "description": "Patient not found" } } } }, "/v1/deepphe-api/deepphe/patient/{patientId}/documents": { "get": { "summary": "Get all documents for a patient", "description": "Returns list of all DocumentXn objects for a specific patient with optional property exclusions.", "tags": [ "DeepPhe" ], "parameters": [ { "in": "path", "name": "patientId", "schema": { "type": "string" }, "required": true, "description": "Patient ID" }, { "in": "query", "name": "documentIds", "schema": { "type": "string" }, "required": false, "description": "Comma-separated list of document IDs to filter by. Only documents matching these IDs will be returned.", "example": "DOC123,DOC456,DOC789" }, { "in": "query", "name": "excludeProperties", "schema": { "type": "string" }, "required": false, "description": "Comma-separated list of DocumentXn properties to exclude from results (e.g., \"mentions,mentionRelations,sections\"). Valid properties: id, name, type, date, episode, text, mentions, mentionRelations, sections", "example": "text,mentionRelations" } ], "responses": { "200": { "description": "List of DocumentXn objects with all properties", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/DocumentXn" } } } } }, "400": { "description": "Missing or invalid patientId" }, "404": { "description": "Patient not found" } } } }, "/v1/deepphe-api/deepphe/patient/{patientId}/documents/episodes": { "get": { "summary": "Get episode counts for patient documents", "description": "Returns an object keyed by normalized episode type with counts for the patient's documents.", "tags": [ "DeepPhe" ], "parameters": [ { "in": "path", "name": "patientId", "schema": { "type": "string" }, "required": true, "description": "Patient ID" }, { "in": "query", "name": "documentIds", "schema": { "type": "string" }, "required": false, "description": "Optional comma-separated list of document IDs to include in the count.", "example": "DOC123,DOC456" } ], "responses": { "200": { "description": "Episode counts keyed by episode type", "content": { "application/json": { "schema": { "type": "object", "additionalProperties": { "type": "integer" } }, "example": { "unknown": 12, "treatment": 6 } } } }, "400": { "description": "Missing or invalid patientId" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/patient/{patientId}/cancers": { "get": { "summary": "Get the cancers file for a patient", "description": "Returns the raw parsed JSON from the {patientId}_Cancers.json key-value entry in the database.", "tags": [ "DeepPhe" ], "parameters": [ { "in": "path", "name": "patientId", "schema": { "type": "string" }, "required": true, "description": "Patient ID" } ], "responses": { "200": { "description": "Cancers data for the patient", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "description": "Missing patientId" }, "404": { "description": "Cancers file not found for this patient" }, "500": { "description": "Internal server error" } } } }, "/v1/deepphe-api/deepphe/patient/{patientId}/concepts": { "get": { "summary": "Get the concepts file for a patient", "description": "Returns the raw parsed JSON from the {patientId}_Concepts.json key-value entry in the database.", "tags": [ "DeepPhe" ], "parameters": [ { "in": "path", "name": "patientId", "schema": { "type": "string" }, "required": true, "description": "Patient ID" } ], "responses": { "200": { "description": "Concepts data for the patient", "content": { "application/json": { "schema": { "type": "object" } } } }, "400": { "description": "Missing patientId" }, "404": { "description": "Concepts file not found for this patient" }, "500": { "description": "Internal server error" } } } } } }