NCBI Datasets REST API — Taxonomy

naftiko: 1.0.0-alpha2
info:
  label: NCBI Datasets REST API — Taxonomy
  description: 'NCBI Datasets REST API — Taxonomy. 1 operations. Lead operation: Get Taxonomy Information. Self-contained
    Naftiko capability covering one United States National Library Of Medicine business surface.'
  tags:
  - United States National Library Of Medicine
  - Taxonomy
  created: '2026-05-19'
  modified: '2026-05-19'
binds:
- namespace: env
  keys:
    UNITED_STATES_NATIONAL_LIBRARY_OF_MEDICINE_API_KEY: UNITED_STATES_NATIONAL_LIBRARY_OF_MEDICINE_API_KEY
capability:
  consumes:
  - type: http
    namespace: ncbi-datasets-taxonomy
    baseUri: https://api.ncbi.nlm.nih.gov/datasets/v2
    description: NCBI Datasets REST API — Taxonomy business capability. Self-contained, no shared references.
    resources:
    - name: taxonomy-taxon-taxons
      path: /taxonomy/taxon/{taxons}
      operations:
      - name: gettaxonomy
        method: GET
        description: Get Taxonomy Information
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: taxons
          in: path
          type: string
          description: Comma-separated taxon names or taxonomy IDs
          required: true
        - name: api_key
          in: query
          type: string
    authentication:
      type: apikey
      key: api_key
      value: '{{env.UNITED_STATES_NATIONAL_LIBRARY_OF_MEDICINE_API_KEY}}'
      placement: query
  exposes:
  - type: rest
    namespace: ncbi-datasets-taxonomy-rest
    port: 8080
    description: REST adapter for NCBI Datasets REST API — Taxonomy. One Spectral-compliant resource per consumed operation,
      prefixed with /v1.
    resources:
    - path: /v1/taxonomy/taxon/{taxons}
      name: taxonomy-taxon-taxons
      description: REST surface for taxonomy-taxon-taxons.
      operations:
      - method: GET
        name: gettaxonomy
        description: Get Taxonomy Information
        call: ncbi-datasets-taxonomy.gettaxonomy
        with:
          taxons: rest.taxons
          api_key: rest.api_key
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    namespace: ncbi-datasets-taxonomy-mcp
    port: 9090
    transport: http
    description: MCP adapter for NCBI Datasets REST API — Taxonomy. One tool per consumed operation, routed inline through
      this capability's consumes block.
    tools:
    - name: get-taxonomy-information
      description: Get Taxonomy Information
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ncbi-datasets-taxonomy.gettaxonomy
      with:
        taxons: tools.taxons
        api_key: tools.api_key
      outputParameters:
      - type: object
        mapping: $.