openapi: 3.0.3
info:
  title: fIVE API
  description: |
    This API allows access to **fIVEDB** (**f**rom **I**n **V**itro **E**xperiments **D**ata **B**ase), 
    a manually curated online database containing the quantitative data on human cells or cell lines obtained _in vitro_ and _ex vivo_. Data processing includes the calculation of parameters suitable for cell process description via mathematical models. 
    **Important!** In order to make a query, all parameters must be chosen from the database dictionaries.
  termsOfService: https://5db.insysbio.com/TermOfUse
  contact:
    email: support@insysbio.com
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  version: 1.0.0
externalDocs:
  description: Find out more about fIVE DB
  url: https://5db.insysbio.com/Index.aspx
servers:
  - url: https://5db.insysbio.com/api/v1
tags:
  - name: process_types
    description: List of process types
  - name: parameters
    description: List of known parameters
  - name: stimulated
    description: List of stimulation conditions
  - name: patient_states
    description: List of known patient states
  - name: products
    description: List of known products
  - name: daughter_cells
    description: List of known daughter cells
  - name: regulators
    description: List of known regulators
  - name: modifiers
    description: List of known modifiers
  - name: query_data
    description: Query result data 
  - name: query_data_headers
    description: Query result headers 

paths:
  /process_types:
    get:
      tags:
        - process_types
      summary: |
        Return full list of the cell process types to be used in Query (optional parameter for query).
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/ProcessType'          
           
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB. 
      security:
        - fivedb_auth:
            - read:process_types
  /parameters:
    get:
      tags:
        - parameters
      summary: |
        Return the list of parameters to be used in Query (optional parameter for query). Parameters are calculated in fIVEDB and describe cell processes.
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Parameter'          
            
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB.
      security:
        - fivedb_auth:
            - read:parameters
  /stimulated:
    get:
      tags:
        - stimulated
      summary: |
        Return the list of cell stimulation conditions (yes/no/no matter). Optional parameter for weighted statistics calculation. If user does not choose option "Calculate weighted statistics" parameter "stimulated" is not used.
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Stimulated'
            
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB.
      security:
        - fivedb_auth:
            - read:stimulated
  /patient_states:
    get:
      tags:
        - patient_states
      summary: |
        Return the list of Patient's states (disease names, severities or additional patients characteristics) to be used in Query (optional parameter for query).
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/PatientState'          
            
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB.
      security:
        - fivedb_auth:
            - read:patient_states
  /products:
    get:
      tags:
        - products
      summary: |
        Return list of products (cytokines and others) secreted by cells to be used in Query (optional parameter for query). Choosing of the cell products are available only for process "Secretion".
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Product'          
            
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB.
      security:
        - fivedb_auth:
            - read:products
  /daughter_cells:
    get:
      tags:
        - daughter_cells
      summary: |
        Return the list of daughter cells to be used in Query (optional parameter for query). Choosing of the daughter cells is available only for process "Differentiation".
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/DaughterCell'          
            
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB.
      security:
        - fivedb_auth:
            - read:daughter_cells
  /regulators:
    get:
      tags:
        - regulators
      summary: |
        Return the list of regulatory molecules (activators or inhibitors which  influence on cell processes) to be used in Query (optional parameter for query). 
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Regulator'          
            
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB.
      security:
        - fivedb_auth:
            - read:regulators            
  /modifiers:
    get:
      tags:
        - modifiers
      summary: |
        Return the list of modifiers to be used in Query (optional parameter for query). Modifiers are molecules which influence on regulators.
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Modifier'          
            
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB.
      security:
        - fivedb_auth:
            - read:modifiers

  /query_data:
    get:
      parameters:
      - name: process_type
        in: query
        description: ''
        required: true
        schema:
          type: string
      - name: parameter
        in: query
        description: ''
        required: true
        schema:
          type: string
      - name: cell_type
        in: query
        description: ''
        schema:
          type: string
      - name: stimulated
        in: query
        description: ''
        schema:
          type: string
      - name: patient_state
        in: query
        description: ''
        schema:
          type: string
      - name: product
        in: query
        description: ''
        schema:
          type: string
      - name: daughter
        in: query
        description: ''
        schema:
          type: string
      - name: regulator
        in: query
        description: ''
        schema:
          type: string
      - name: modifier
        in: query
        description: ''
        schema:
          type: string
      - name: wstatSwitch
        in: query
        description: 'true  - only weighted result or false - all data without weighted result'
        schema:
          type: string
      - name: headers
        in: query
        description: 'comma separated list of params to output to result'
        schema:
          type: string
      tags:
        - query_data
      summary: |
        Return the list with query output according to parameters provided.
        There are a total of 11 parameters, where multiple inputs can be selected for all parameters, but currently,
        only the "OR" logic is supported.
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/QueryData'          
            
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB.
      security:
        - fivedb_auth:
            - read:query_data

  /query_data_headers:
    get:
      tags:
        - query_data_headers
      summary: |
        Return the list with query headers, where multiple inputs can be selected for all parameters, but currently,
        only the "OR" logic is supported.
      responses:
        '200':
          description: successful operation
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/QueryDataHeader'          
            
        '400':
          description: Invalid status value. This response appears when the required object does not exist in the DB.
      security:
        - fivedb_auth:
            - read:query_data_headers
components:
  schemas:
    ProcessType:
      required:
        - name
        - id
      type: object
      properties:
        id:
          type: integer
          format: int64
          example: 10
        name:
          type: string
          example: Secretion
          description: Process type name available
      
    Parameter:
      required:
        - name
        - id
      type: object
      properties:
        id:
          type: integer
          format: int64
          example: 10
        name:
          type: string
          description: Parameter name available
          example: kbase
     
    Stimulated:
      required:
        - name
        - id
      type: object
      properties:
        id:
          type: integer
          format: int64
          example: 10
        name:
          type: string
          description: Stimulated name available
          example: No
      
    PatientState:
      required:
        - name
        - id
      type: object
      properties:
        id:
          type: integer
          format: int64
          example: 10
        name:
          type: string
          description: Patient state available
          example: Healthy

    Product:
      required:
        - name
        - id
      type: object
      properties:
        id:
          type: integer
          format: int64
          example: 10
        name:
          type: string
          description: Product
          example: IL6
      
    DaughterCell:
      required:
        - name
        - id
      type: object
      properties:
        id:
          type: integer
          format: int64
          example: 10
        name:
          type: string
          description: Daughter cell name used
          example: Granulocytes
      
    Regulator:
      required:
        - name
        - id
      type: object
      properties:
        id:
          type: integer
          format: int64
          example: 10
        name:
          type: string
          description: Regulator name used
          example: TNF

    Modifier:
      required:
        - name
        - id
      type: object
      properties:
        id:
          type: integer
          format: int64
          example: 10
        name:
          type: string
          description: Modifier name used
          example: IL17

    QueryDataHeader:
      type: object
      properties:
        ColumnVariable:
          type: string
          description: 'column variable name'
        ColumnDesc:
          type: string
          description: 'column description'

    QueryData:
      required:
        - s_name
        - s_val
        - u_base
      type: object
      properties:
        prm_name:
          type: string
          description: Parameter
          example: Parameter
        prm_val_unf:
          type: string
          description: Unified Parameter value
          example: Unified Parameter value
        prm_val:
          type: string
          description: Parameter value
          example: Parameter value
        prm_unt:
          type: string
          description: Parameter unit
          example: Parameter unit
        pro_name:
          type: string
          description: Process type
          example: Process type
        stm_cell:
          type: string
          description: Stimulated cells
          example: Stimulated cells
        c_name:
          type: string
          description: Cell type
          example: Cell type
        prd_name:
          type: string
          description: Cell product
          example: Cell product
        prd_name_db:
          type: string
          description: Cell product DB name
          example: Cell product DB name
        prd_mw:
          type: string
          description: Product Mw(kDa)
          example: Product Mw(kDa)
        dt_name:
          type: string
          description: Daughter cells
          example: Daughter cells
        n_val:
          type: string
          description: 'N of in vitro experiments'
          example: 'N of in vitro experiments'
        avg_type:
          type: string
          description: 'Average type'
          example: 'Average type'
        exp_val:
          type: string
          description: 'Experimental value'
          example: 'Experimental value'
        dsp_type:
          type: string
          description: 'Dispersion type'
          example: 'Dispersion type'
        dsp_left:
          type: string
          description: 'Dispersion left'
          example: 'Dispersion left'
        dsp_right:
          type: string
          description: 'Dispersion right'
          example: 'Dispersion right'
        exp_val_unt:
          type: string
          description: 'Experimental value unit'
          example: 'Experimental value unit'
        exp_res:
          type: string
          description: 'Experiment result type'
          example: 'Experiment result type'
        r_name:
          type: string
          description: 'Regulator'
          example: 'Regulator'
        r_name_db:
          type: string
          description: 'Regulator DB name'
          example: 'Regulator DB name'
        r_mw:
          type: string
          description: 'Regulator Mw(kDa)'
          example: 'Regulator Mw(kDa)'
        reg_con:
          type: string
          description: 'Regulator concentration'
          example: 'Regulator concentration'
        reg_con_unt:
          type: string
          description: 'Regulator concentration unit'
          example: 'Regulator concentration unit'
        m_name:
          type: string
          description: 'Modifier'
          example: 'Modifier'
        m_name_db:
          type: string
          description: 'Modifier DB name'
          example: 'Modifier DB name'
        m_mw:
          type: string
          description: 'Modifier Mw(kDa)'
          example: 'Modifier Mw(kDa)'
        mod_con:
          type: string
          description: 'Modifier concentration'
          example: 'Modifier concentration'
        mod_con_unt:
          type: string
          description: 'Modifier concentration unit'
          example: 'Modifier concentration unit'
        exp_t:
          type: string
          description: 'Experiment time'
          example: 'Experiment time'
        exp_u:
          type: string
          description: 'Experiment time unit'
          example: 'Experiment time unit'
        cell_con:
          type: string
          description: 'Initial cell concentration'
          example: 'Initial cell concentration'
        cell_con_unt:
          type: string
          description: 'Initial cell concentration unit'
          example: 'Initial cell concentration unit'
        t_name:
          type: string
          description: 'Source of cells'
          example: 'Source of cells'
        c_line:
          type: string
          description: 'Cell line/primary cells'
          example: 'Cell line/primary cells'
        ser_phc:
          type: string
          description: 'Cell phenotype'
          example: 'Cell phenotype'
        ser_cm:
          type: string
          description: 'Culture media'
          example: 'Culture media'
        ser_stmln:
          type: string
          description: 'Stimulation'
          example: 'Stimulation'
        ser_comment:
          type: string
          description: 'Commentary'
          example: 'Commentary'
        d_name:
          type: string
          description: 'Patient’s state'
          example: 'Patient’s state'
        ser_age:
          type: string
          description: 'Age category'
          example: 'Age category'
        pmid:
          type: string
          description: 'Article PMID'
          example: 'Article PMID'

  securitySchemes:
    fivedb_auth:
      type: oauth2
      flows:
        implicit:
          authorizationUrl: https://5db.insysbio.com/oauth/token
          scopes:
            read:process_types: read process types
            read:parameters: read parameters
            read:stimulated: read stimulated
            read:patient_states: read patient states
            read:products: read products
            read:daughter_cells: read daughter cells
            read:regulators: read regulators
            read:modifiers: read modifiers
            read:query_data: read query data
            read:query_data_headers: read query data headers
    api_key:
      type: apiKey
      name: Authorization
      in: header