schema.yml

openapi: 3.0.3
info:
  title: Modulector
  version: 2.2.1
  description: "\n### An open platform which provides information about methylation\
    \ sites, miRNAs and genes from different popular databases.  \nThe platform is\
    \ part of the Multiomix project. For more information, visit our [website](https://omicsdatascience.org/).\n\
    To contribute: [OmicsDatascience](https://github.com/omics-datascience/modulector)"
paths:
  /diseases/:
    get:
      operationId: diseases_list
      description: This service provides information, with evidence supported by experiments,
        on the relationships between miRNAs and human diseases.
      summary: Relationship between miRNAs and human diseases
      parameters:
      - in: query
        name: mirna
        schema:
          type: string
        description: miRNA (miRNA code or Accession ID) to get its interactions with
          different targets. If it is not specified, the service returns all the elements
          in a paginated response.
        examples:
          ? ''
          : value: ''
          Hsa-miR-891a-5p:
            value: hsa-miR-891a-5p
            summary: hsa-miR-891a-5p
          Hsa-miR-21-5p:
            value: hsa-miR-21-5p
            summary: hsa-miR-21-5p
      - in: query
        name: search
        schema:
          type: string
        description: Search by disease name
        examples:
          ? ''
          : value: ''
          BreastNeoplasms:
            value: Breast Neoplasms
            summary: Breast Neoplasms
          Atherosclerosis:
            value: Atherosclerosis
      tags:
      - miRNA
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedMirnaDiseaseList'
          description: ''
  /drugs/:
    get:
      operationId: drugs_list
      description: Returns a paginated response of experimentally validated small
        molecules (or drugs) that affect miRNA expression.
      summary: Provides a list of drugs affecting miRNA expression.
      parameters:
      - in: query
        name: fda_approved
        schema:
          type: boolean
        description: Defines if the drug is approved by the FDA
      - in: query
        name: mirna
        schema:
          type: string
        description: miRNA (miRNA code or Accession ID) to get its interactions with
          different targets. If it is not specified, the service returns all the elements
          in a paginated response.
        examples:
          ? ''
          : value: ''
          MiR-126*:
            value: miR-126*
            summary: miR-126*
          MiR-21:
            value: miR-21
            summary: miR-21
          MiR-155:
            value: miR-155
            summary: miR-155
      - in: query
        name: search
        schema:
          type: string
        description: Search by condition, small_molecule, and expression_pattern
        examples:
          ? ''
          : value: ''
          Arsenite:
            value: Arsenite
          Up-regulated:
            value: up-regulated
            summary: up-regulated
      tags:
      - miRNA
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedMirnaDrugsList'
          description: ''
  /methylation/:
    get:
      operationId: methylation_retrieve
      description: |-
        Service that obtains information about a specific CpG methylation site from
        the 'Infinium MethylationEPIC V2.0' array.
      summary: Retrieve methylation details
      parameters:
      - in: query
        name: methylation_site
        schema:
          type: string
        description: Methylation site name from Illumina Infinium MethylationEPIC
          2.0 array
        required: true
        examples:
          Cg22461615:
            value: cg22461615
            summary: cg22461615
          Cg00000029:
            value: cg00000029
            summary: cg00000029
      tags:
      - Methylation
      responses:
        '200':
          description: No response body
  /methylation-sites/:
    post:
      operationId: methylation_sites_create
      description: |-
        Service that searches a list of methylation site identifiers from different Illumina array versions and
        returns the identifiers for the most recent version of the array.
      summary: Retrieve Methylation sites
      tags:
      - Methylation
      requestBody:
        content:
          application/json:
            schema:
              schema:
                type: object
                properties:
                  methylation_sites:
                    type: array
                    items:
                      type: string
                    description: List of Methylation names.
                required:
                - methylation_sites
              example:
                methylation_sites:
                - cg17771854_BC11
                - cg01615704_TC11
      responses:
        '200':
          description: No response body
  /methylation-sites-finder/:
    get:
      operationId: methylation_sites_finder_retrieve
      description: |-
        Service that takes a text string of any length and returns a list of methylation site names (loci) containing
        that search criteria within the Illumina 'Infinium MethylationEPIC' array.
      summary: Searches and lists Methylation sites matching a string.
      parameters:
      - in: query
        name: limit
        schema:
          type: integer
        description: number of elements returned by the service. 50 by default and
          a maximum of 3000.
      - in: query
        name: query
        schema:
          type: string
        description: Methylation search string.
        examples:
          ? ''
          : value: ''
          Cg25:
            value: cg25
            summary: cg25
          Cg01:
            value: cg01
            summary: cg01
      tags:
      - Methylation
      responses:
        '200':
          description: No response body
  /methylation-sites-genes/:
    post:
      operationId: methylation_sites_genes_create
      description: |-
        A service that searches a list of CpG methylation site identifiers from different
        versions of Illumina arrays and returns the gene(s) they belong to.
      summary: Retrieve genes from methylation sites
      tags:
      - Methylation
      requestBody:
        content:
          application/json:
            schema:
              schema:
                type: object
                properties:
                  methylation_sites:
                    type: array
                    items:
                      type: string
                    description: list of Illumina array methylation site names or
                      identifiers for which you want to know the gene(s).
                required:
                - methylation_sites
              example:
                methylation_sites:
                - cg17771854_BC11
                - cg22461615_TC11
                - name_007
      responses:
        '200':
          description: No response body
  /mirna/:
    get:
      operationId: mirna_list
      description: This functionality allows obtaining different information about
        a miRNA, such as its sequence, its previous identifiers and databases where
        information about it can be found.
      summary: Retrieves miRNA details, including sequence, identifiers, and related
        databases.
      parameters:
      - in: query
        name: mirna
        schema:
          type: string
        description: miRNA identifier (miRNA code or Accession ID).
        examples:
          ? ''
          : value: ''
          Hsa-miR-548ai:
            value: hsa-miR-548ai
            summary: hsa-miR-548ai
          Hsa-miR-21-5p:
            value: hsa-miR-21-5p
            summary: hsa-miR-21-5p
      tags:
      - miRNA
      responses:
        '200':
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Mirna'
          description: ''
  /mirna-aliases/:
    get:
      operationId: mirna_aliases_list
      description: Returns all associations between miRNAs Accessions IDs (MIMAT)
        and miRNAs matures IDs from the miRBase database.
      summary: Lists miRNA Accession and mature IDs from miRBase.
      parameters:
      - in: query
        name: mature_mirna
        schema:
          type: string
        description: Use to show only a specific miRNAs matures ID.
        examples:
          ? ''
          : value: ''
          Hsa-miR-21-5p:
            value: hsa-miR-21-5p
            summary: hsa-miR-21-5p
          Hsa-miR-155-5p:
            value: hsa-miR-155-5p
            summary: hsa-miR-155-5p
      - in: query
        name: mirbase_accession_id
        schema:
          type: string
        description: Use to show only a specific miRNAs Accession ID.
        examples:
          ? ''
          : value: ''
          MIMAT0000062:
            value: MIMAT0000062
          MIMAT0000063:
            value: MIMAT0000063
      tags:
      - miRNA
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedMirnaAliasesList'
          description: ''
  /mirna-codes/:
    post:
      operationId: mirna_codes_create
      description: Service that searches a list of miRNA codes and returns the code
        for the miRbase DB.
      summary: Retrieve miRNA codes
      tags:
      - miRNA
      requestBody:
        content:
          application/json:
            schema:
              schema:
                type: object
                properties:
                  mirna_codes:
                    type: array
                    items:
                      type: string
                    description: List of miRNA Previous IDs or Accession IDs to retrieve
                      the associated Accession IDs.
                required:
                - mirna_codes
              example:
                mirna_codes:
                - name_01
                - hsa-miR-487a-3p
                - MIMAT0000066
                - MI0026417
                - hsa-let-7e-5p
      responses:
        '200':
          description: No response body
  /mirna-codes-finder/:
    get:
      operationId: mirna_codes_finder_retrieve
      description: Service that takes a string of any length and returns a list of
        miRNA ids that contain that search criteria.
      summary: Searches and lists miRNAs matching a string.
      parameters:
      - in: query
        name: limit
        schema:
          type: integer
        description: number of elements returned by the service. 50 by default and
          a maximum of 3000.
      - in: query
        name: query
        schema:
          type: string
        description: miRNA search string.
        examples:
          ? ''
          : value: ''
          Hsa-miR-2:
            value: hsa-miR-2
            summary: hsa-miR-2
          Hsa-miR-1:
            value: hsa-miR-1
            summary: hsa-miR-1
      tags:
      - miRNA
      responses:
        '200':
          description: No response body
  /mirna-target-interactions/:
    get:
      operationId: mirna_target_interactions_list
      description: Receives a miRNA and/or a gene symbol and returns a paginated vector.
        Each vector entry represents a miRNA-Gene interaction. If no gene symbol is
        entered, all miRNA interactions are returned. If a miRNA is not entered, all
        gene interactions are returned. If both are entered, the interaction of mirna
        with the gene is returned.
      summary: Retrieve miRNA interactions
      parameters:
      - in: query
        name: gene
        schema:
          type: string
        description: Gene symbol to get its interactions with different miRNA targets
        examples:
          EGFR:
            value: EGFR
          APPBP2:
            value: APPBP2
      - in: query
        name: include_pubmeds
        schema:
          type: boolean
        description: If True, the endpoint also returns a list of links to Pubmed
          where the miRNAs are related to the genes (this may affect Modulector's
          response time)
      - in: query
        name: mirna
        schema:
          type: string
        description: miRNA (Accession ID or name in mirBase) to get its interactions
          with different gene targets.
        required: true
        examples:
          Hsa-miR-891a-5p:
            value: hsa-miR-891a-5p
            summary: hsa-miR-891a-5p
          Hsa-miR-891a-3p:
            value: hsa-miR-891a-3p
            summary: hsa-miR-891a-3p
      - in: query
        name: score
        schema:
          type: number
          format: double
        description: Numerical score to filter the interactions (only interactions
          with a score greater than or equal to the parameter value are returned).
      tags:
      - miRNA
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedMirnaXGenList'
          description: ''
components:
  schemas:
    Mirna:
      type: object
      properties:
        aliases:
          type: array
          items:
            type: string
          description: |-
            Gets a miRNA aliases.
            :param mirna: miRNA object to get its aliases.
            :return: List of miRNA aliases.
          readOnly: true
        mirna_sequence:
          type: string
          nullable: true
          maxLength: 40
        mirbase_accession_id:
          type: string
          readOnly: true
        links:
          type: array
          items:
            type: object
            additionalProperties: {}
          description: |-
            Gets a list of sources links for a specific miRNA.
            :param mirna: miRNA object.
            :return: List of sources links.
          readOnly: true
      required:
      - aliases
      - links
      - mirbase_accession_id
    MirnaAliases:
      type: object
      properties:
        mirbase_accession_id:
          type: string
          maxLength: 20
        mature_mirna:
          type: string
          maxLength: 30
      required:
      - mature_mirna
      - mirbase_accession_id
    MirnaDisease:
      type: object
      properties:
        id:
          type: integer
          readOnly: true
        category:
          type: string
          maxLength: 200
        disease:
          type: string
          maxLength: 200
        pubmed:
          type: string
          description: |-
            Gets a PubMed URL for a miRNA-disease association.
            :param disease: MirnaDisease object.
            :return: Pubmed URL.
          readOnly: true
        description:
          type: string
      required:
      - category
      - description
      - disease
      - id
      - pubmed
    MirnaDrugs:
      type: object
      properties:
        id:
          type: integer
          readOnly: true
        small_molecule:
          type: string
        fda_approved:
          type: boolean
        detection_method:
          type: string
          maxLength: 100
        condition:
          type: string
        pubmed:
          type: string
          description: |-
            Gets a Pubmed URL for a miRNA-drug association
            :param drug: MirnaDrugs object
            :return: Pubmed URL
          readOnly: true
        reference:
          type: string
        expression_pattern:
          type: string
          maxLength: 30
        support:
          type: string
      required:
      - condition
      - detection_method
      - expression_pattern
      - fda_approved
      - id
      - pubmed
      - reference
      - small_molecule
      - support
    MirnaXGen:
      type: object
      properties:
        id:
          type: integer
          readOnly: true
        mirna:
          type: string
          readOnly: true
        gene:
          type: string
          maxLength: 50
        score:
          type: string
          format: decimal
          pattern: ^-?\d{0,16}(?:\.\d{0,4})?$
        source_name:
          type: string
          readOnly: true
        pubmeds:
          type: array
          items:
            type: string
          description: |-
            Gets a list of related Pubmed URLs to a miRNA-Gene interaction.
            :param mirna_gene_interaction: miRNA-Gene interaction.
            :return: List of Pubmed URLs.
          readOnly: true
        sources:
          type: array
          items:
            type: string
          description: |-
            Gets a list of sources for a miRNA-Gene interaction
            :param mirna_gene_interaction: miRNA-Gene interaction
            :return: List of sources for the interaction
          readOnly: true
        score_class:
          type: string
          nullable: true
          maxLength: 3
      required:
      - gene
      - id
      - mirna
      - pubmeds
      - score
      - source_name
      - sources
    PaginatedMirnaAliasesList:
      type: object
      properties:
        count:
          type: integer
          example: 123
        next:
          type: string
          nullable: true
          format: uri
          example: http://api.example.org/accounts/?page=4
        previous:
          type: string
          nullable: true
          format: uri
          example: http://api.example.org/accounts/?page=2
        results:
          type: array
          items:
            $ref: '#/components/schemas/MirnaAliases'
    PaginatedMirnaDiseaseList:
      type: object
      properties:
        count:
          type: integer
          example: 123
        next:
          type: string
          nullable: true
          format: uri
          example: http://api.example.org/accounts/?page=4
        previous:
          type: string
          nullable: true
          format: uri
          example: http://api.example.org/accounts/?page=2
        results:
          type: array
          items:
            $ref: '#/components/schemas/MirnaDisease'
    PaginatedMirnaDrugsList:
      type: object
      properties:
        count:
          type: integer
          example: 123
        next:
          type: string
          nullable: true
          format: uri
          example: http://api.example.org/accounts/?page=4
        previous:
          type: string
          nullable: true
          format: uri
          example: http://api.example.org/accounts/?page=2
        results:
          type: array
          items:
            $ref: '#/components/schemas/MirnaDrugs'
    PaginatedMirnaXGenList:
      type: object
      properties:
        count:
          type: integer
          example: 123
        next:
          type: string
          nullable: true
          format: uri
          example: http://api.example.org/accounts/?page=4
        previous:
          type: string
          nullable: true
          format: uri
          example: http://api.example.org/accounts/?page=2
        results:
          type: array
          items:
            $ref: '#/components/schemas/MirnaXGen'