> ## Documentation Index
> Fetch the complete documentation index at: https://docs.rafflesia.ai/llms.txt
> Use this file to discover all available pages before exploring further.

# List searchable homology databases

> Returns one cursor page of the homology databases available to search, each with its molecule type, the query kinds it accepts, the evidence it can return, and the immutable release its default alias resolves to when one is published. A search always executes against a release id, never against a mutable alias.



## OpenAPI

````yaml /api-reference/openapi.json get /v1/homology/databases
openapi: 3.1.0
info:
  description: >-
    Deterministic biological evidence primitives. Every response is the same
    envelope: ok, data, warnings, provenance.
  title: Rafflesia API
  version: 0.1.0
servers:
  - description: Production
    url: https://api.rafflesia.ai
security:
  - bearerAuth: []
paths:
  /v1/homology/databases:
    get:
      tags:
        - Homology
      summary: List searchable homology databases
      description: >-
        Returns one cursor page of the homology databases available to search,
        each with its molecule type, the query kinds it accepts, the evidence it
        can return, and the immutable release its default alias resolves to when
        one is published. A search always executes against a release id, never
        against a mutable alias.
      operationId: homology_databases_list
      parameters:
        - explode: false
          in: query
          name: limit
          schema:
            default: 20
            format: int64
            maximum: 100
            minimum: 1
            type: integer
        - explode: false
          in: query
          name: starting_after
          schema:
            type: string
        - explode: false
          in: query
          name: ending_before
          schema:
            type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/EnvelopeHomologyDatabaseList'
          description: OK
          headers:
            Rafflesia-Contract-Digest:
              schema:
                type: string
            Rafflesia-Version:
              schema:
                type: string
            X-Request-ID:
              schema:
                type: string
        default:
          content:
            application/problem+json:
              schema:
                $ref: '#/components/schemas/ErrorModel'
          description: Error
components:
  schemas:
    EnvelopeHomologyDatabaseList:
      additionalProperties: false
      properties:
        $schema:
          description: A URL to the JSON Schema for this object.
          examples:
            - https://example.com/schemas/EnvelopeHomologyDatabaseList.json
          format: uri
          readOnly: true
          type: string
        data:
          $ref: '#/components/schemas/HomologyDatabaseList'
          description: Operation result data.
        error:
          $ref: '#/components/schemas/APIError'
          description: Structured error information.
        evidence:
          $ref: '#/components/schemas/EvidenceSummary'
          description: Mechanical evidence summary for agent inspection and chaining.
        ok:
          description: Whether the operation succeeded.
          type: boolean
        provenance:
          $ref: '#/components/schemas/Provenance'
          description: Execution provenance.
        warnings:
          description: Non-fatal warnings.
          items:
            $ref: '#/components/schemas/Warning'
          type:
            - array
            - 'null'
      required:
        - ok
        - warnings
        - provenance
      type: object
    ErrorModel:
      additionalProperties: false
      properties:
        $schema:
          description: A URL to the JSON Schema for this object.
          examples:
            - https://example.com/schemas/ErrorModel.json
          format: uri
          readOnly: true
          type: string
        detail:
          description: >-
            A human-readable explanation specific to this occurrence of the
            problem.
          examples:
            - Property foo is required but is missing.
          type: string
        errors:
          description: Optional list of individual error details
          items:
            $ref: '#/components/schemas/ErrorDetail'
          type:
            - array
            - 'null'
        instance:
          description: >-
            A URI reference that identifies the specific occurrence of the
            problem.
          examples:
            - https://example.com/error-log/abc123
          format: uri
          type: string
        status:
          description: HTTP status code
          examples:
            - 400
          format: int64
          type: integer
        title:
          description: >-
            A short, human-readable summary of the problem type. This value
            should not change between occurrences of the error.
          examples:
            - Bad Request
          type: string
        type:
          default: about:blank
          description: A URI reference to human-readable documentation for the error.
          examples:
            - https://example.com/errors/example
          format: uri
          type: string
      type: object
    HomologyDatabaseList:
      additionalProperties: false
      properties:
        data:
          items:
            $ref: '#/components/schemas/HomologyDatabase'
          type:
            - array
            - 'null'
        has_more:
          type: boolean
        next_cursor:
          type: string
        object:
          description: Always list.
          type: string
        url:
          type: string
      required:
        - object
        - url
        - data
        - has_more
      type: object
    APIError:
      additionalProperties: false
      properties:
        code:
          description: Stable specific error code.
          type: string
        details:
          additionalProperties: {}
          description: Additional structured error details.
          type: object
        doc_url:
          description: Stable documentation URL for this error code.
          type: string
        message:
          description: Human-readable error message.
          type: string
        param:
          description: Request field responsible for the error when known.
          type: string
        type:
          description: Stable coarse error category.
          enum:
            - invalid_request_error
            - resource_missing
            - resource_expired
            - conflict_error
            - rate_limit_error
            - authentication_error
            - permission_error
            - billing_error
            - api_error
          type: string
      required:
        - type
        - code
        - message
        - doc_url
      type: object
    EvidenceSummary:
      additionalProperties: false
      properties:
        duration_ms:
          description: >-
            Primary elapsed duration in milliseconds when the response exposes
            one.
          format: int64
          type: integer
        input_refs:
          description: >-
            Input references detected from request fields such as object_id,
            structure_id, target_id, and sequence_id.
          items:
            type: string
          type:
            - array
            - 'null'
        object_refs:
          description: Object ids or object refs visible in the response/provenance.
          items:
            type: string
          type:
            - array
            - 'null'
        output_refs:
          description: Output references detected from response data and generated objects.
          items:
            type: string
          type:
            - array
            - 'null'
        row_count:
          description: >-
            Primary row count or returned row count when the response exposes
            one.
          format: int64
          type: integer
        warnings_count:
          description: Number of non-fatal warnings in the envelope.
          format: int64
          type: integer
      required:
        - warnings_count
      type: object
    Provenance:
      additionalProperties: false
      properties:
        cache_hit:
          description: Whether cached output was reused.
          type: boolean
        created_at:
          description: UTC timestamp.
          type: string
        database_snapshots:
          description: Database snapshots used.
          items:
            $ref: '#/components/schemas/DatabaseSnapshot'
          type:
            - array
            - 'null'
        generated_object_ids:
          description: Object ids created by the operation.
          items:
            type: string
          type:
            - array
            - 'null'
        input_hash:
          description: SHA-256 hash of canonical request input.
          type: string
        operation:
          description: Primitive operation id.
          type: string
        parameters_hash:
          description: SHA-256 hash of parameters.
          type: string
        request_id:
          description: Unique request identifier.
          type: string
        server_version:
          description: Server version.
          type: string
        tool_versions:
          description: Tool versions used.
          items:
            $ref: '#/components/schemas/ToolVersion'
          type:
            - array
            - 'null'
      required:
        - request_id
        - operation
        - created_at
        - server_version
      type: object
    Warning:
      additionalProperties: false
      properties:
        code:
          description: Stable warning code.
          type: string
        details:
          additionalProperties: {}
          description: Additional structured warning details.
          type: object
        message:
          description: Human-readable warning message.
          type: string
      required:
        - code
        - message
      type: object
    ErrorDetail:
      additionalProperties: false
      properties:
        location:
          description: >-
            Where the error occurred, e.g. 'body.items[3].tags' or
            'path.thing-id'
          type: string
        message:
          description: Error message text
          type: string
        value:
          description: The value at the given location
      type: object
    HomologyDatabase:
      additionalProperties: false
      properties:
        default_release_alias:
          type: string
        default_release_id:
          description: Immutable release currently selected by the default alias.
          type: string
        description:
          type: string
        display_name:
          type: string
        evidence:
          items:
            type: string
          type:
            - array
            - 'null'
        id:
          description: Opaque database id used to enumerate immutable releases.
          type: string
        molecule_type:
          type: string
        object:
          description: Always homology_database.
          type: string
        query_kinds:
          items:
            type: string
          type:
            - array
            - 'null'
        slug:
          description: Human-readable stable database slug.
          type: string
      required:
        - object
        - id
        - slug
        - display_name
        - molecule_type
        - query_kinds
        - evidence
      type: object
    DatabaseSnapshot:
      additionalProperties: false
      properties:
        digest:
          type: string
        kind:
          type: string
        name:
          type: string
        version:
          type: string
      required:
        - name
        - version
      type: object
    ToolVersion:
      additionalProperties: false
      properties:
        name:
          type: string
        path:
          type: string
        version:
          type: string
      required:
        - name
        - version
      type: object
  securitySchemes:
    bearerAuth:
      description: 'A Rafflesia API key, sent as `Authorization: Bearer <key>`.'
      scheme: bearer
      type: http

````