NCBI Datasets REST API — Genome

naftiko: 1.0.0-alpha2
info:
  label: NCBI Datasets REST API — Genome
  description: 'NCBI Datasets REST API — Genome. 2 operations. Lead operation: Get Genome by Accession. Self-contained Naftiko
    capability covering one United States National Library Of Medicine business surface.'
  tags:
  - United States National Library Of Medicine
  - Genome
  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-genome
    baseUri: https://api.ncbi.nlm.nih.gov/datasets/v2
    description: NCBI Datasets REST API — Genome business capability. Self-contained, no shared references.
    resources:
    - name: genome-accession-accessions-dataset_report
      path: /genome/accession/{accessions}/dataset_report
      operations:
      - name: getgenomebyaccession
        method: GET
        description: Get Genome by Accession
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: accessions
          in: path
          type: string
          description: Comma-separated assembly accession numbers
          required: true
        - name: api_key
          in: query
          type: string
    - name: genome-taxon-taxons-dataset_report
      path: /genome/taxon/{taxons}/dataset_report
      operations:
      - name: getgenomedatasetreport
        method: GET
        description: Get Genome Dataset Report
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: taxons
          in: path
          type: string
          description: Comma-separated list of taxa (species names, common names, or NCBI taxonomy IDs)
          required: true
        - name: api_key
          in: query
          type: string
          description: NCBI API key for increased rate limits
        - name: filters.assembly_level
          in: query
          type: array
          description: Filter by assembly level
        - name: filters.assembly_source
          in: query
          type: string
          description: Filter by assembly source
        - name: page_size
          in: query
          type: integer
          description: Number of results per page (max 1000)
        - name: page_token
          in: query
          type: string
          description: Token for the next page of results
    authentication:
      type: apikey
      key: api_key
      value: '{{env.UNITED_STATES_NATIONAL_LIBRARY_OF_MEDICINE_API_KEY}}'
      placement: query
  exposes:
  - type: rest
    namespace: ncbi-datasets-genome-rest
    port: 8080
    description: REST adapter for NCBI Datasets REST API — Genome. One Spectral-compliant resource per consumed operation,
      prefixed with /v1.
    resources:
    - path: /v1/genome/accession/{accessions}/dataset-report
      name: genome-accession-accessions-dataset-report
      description: REST surface for genome-accession-accessions-dataset_report.
      operations:
      - method: GET
        name: getgenomebyaccession
        description: Get Genome by Accession
        call: ncbi-datasets-genome.getgenomebyaccession
        with:
          accessions: rest.accessions
          api_key: rest.api_key
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/genome/taxon/{taxons}/dataset-report
      name: genome-taxon-taxons-dataset-report
      description: REST surface for genome-taxon-taxons-dataset_report.
      operations:
      - method: GET
        name: getgenomedatasetreport
        description: Get Genome Dataset Report
        call: ncbi-datasets-genome.getgenomedatasetreport
        with:
          taxons: rest.taxons
          api_key: rest.api_key
          filters.assembly_level: rest.filters.assembly_level
          filters.assembly_source: rest.filters.assembly_source
          page_size: rest.page_size
          page_token: rest.page_token
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    namespace: ncbi-datasets-genome-mcp
    port: 9090
    transport: http
    description: MCP adapter for NCBI Datasets REST API — Genome. One tool per consumed operation, routed inline through this
      capability's consumes block.
    tools:
    - name: get-genome-accession
      description: Get Genome by Accession
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ncbi-datasets-genome.getgenomebyaccession
      with:
        accessions: tools.accessions
        api_key: tools.api_key
      outputParameters:
      - type: object
        mapping: $.
    - name: get-genome-dataset-report
      description: Get Genome Dataset Report
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ncbi-datasets-genome.getgenomedatasetreport
      with:
        taxons: tools.taxons
        api_key: tools.api_key
        filters.assembly_level: tools.filters.assembly_level
        filters.assembly_source: tools.filters.assembly_source
        page_size: tools.page_size
        page_token: tools.page_token
      outputParameters:
      - type: object
        mapping: $.