NCBI E-Utilities API — Search

naftiko: 1.0.0-alpha2
info:
  label: NCBI E-Utilities API — Search
  description: 'NCBI E-Utilities API — Search. 2 operations. Lead operation: Search Entrez Database. Self-contained Naftiko
    capability covering one United States National Library Of Medicine business surface.'
  tags:
  - United States National Library Of Medicine
  - Search
  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-e-utilities-search
    baseUri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils
    description: NCBI E-Utilities API — Search business capability. Self-contained, no shared references.
    resources:
    - name: esearch.fcgi
      path: /esearch.fcgi
      operations:
      - name: searchdatabase
        method: GET
        description: Search Entrez Database
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: db
          in: query
          type: string
          description: Target Entrez database (e.g. pubmed, nuccore, protein, gene, snp, mesh, pmc)
          required: true
        - name: term
          in: query
          type: string
          description: Entrez text query with optional field tags and Boolean operators
          required: true
        - name: api_key
          in: query
          type: string
          description: NCBI API key for increased rate limits
        - name: retmax
          in: query
          type: integer
          description: Maximum number of UIDs to return (default 20, max 10000)
        - name: retstart
          in: query
          type: integer
          description: Index of first UID in results (for pagination)
        - name: retmode
          in: query
          type: string
          description: Output format
        - name: sort
          in: query
          type: string
          description: Sort order for results
        - name: datetype
          in: query
          type: string
          description: Date type for date range filtering
        - name: mindate
          in: query
          type: string
          description: Minimum date for range filter (YYYY/MM/DD)
        - name: maxdate
          in: query
          type: string
          description: Maximum date for range filter (YYYY/MM/DD)
        - name: usehistory
          in: query
          type: string
          description: Store results on NCBI server (y/n)
    - name: espell.fcgi
      path: /espell.fcgi
      operations:
      - name: checkspelling
        method: GET
        description: Check Query Spelling
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: db
          in: query
          type: string
          description: Target Entrez database
          required: true
        - name: term
          in: query
          type: string
          description: Query term to check spelling for
          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-e-utilities-search-rest
    port: 8080
    description: REST adapter for NCBI E-Utilities API — Search. One Spectral-compliant resource per consumed operation, prefixed
      with /v1.
    resources:
    - path: /v1/esearch-fcgi
      name: esearch-fcgi
      description: REST surface for esearch.fcgi.
      operations:
      - method: GET
        name: searchdatabase
        description: Search Entrez Database
        call: ncbi-e-utilities-search.searchdatabase
        with:
          db: rest.db
          term: rest.term
          api_key: rest.api_key
          retmax: rest.retmax
          retstart: rest.retstart
          retmode: rest.retmode
          sort: rest.sort
          datetype: rest.datetype
          mindate: rest.mindate
          maxdate: rest.maxdate
          usehistory: rest.usehistory
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/espell-fcgi
      name: espell-fcgi
      description: REST surface for espell.fcgi.
      operations:
      - method: GET
        name: checkspelling
        description: Check Query Spelling
        call: ncbi-e-utilities-search.checkspelling
        with:
          db: rest.db
          term: rest.term
          api_key: rest.api_key
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    namespace: ncbi-e-utilities-search-mcp
    port: 9090
    transport: http
    description: MCP adapter for NCBI E-Utilities API — Search. One tool per consumed operation, routed inline through this
      capability's consumes block.
    tools:
    - name: search-entrez-database
      description: Search Entrez Database
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ncbi-e-utilities-search.searchdatabase
      with:
        db: tools.db
        term: tools.term
        api_key: tools.api_key
        retmax: tools.retmax
        retstart: tools.retstart
        retmode: tools.retmode
        sort: tools.sort
        datetype: tools.datetype
        mindate: tools.mindate
        maxdate: tools.maxdate
        usehistory: tools.usehistory
      outputParameters:
      - type: object
        mapping: $.
    - name: check-query-spelling
      description: Check Query Spelling
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ncbi-e-utilities-search.checkspelling
      with:
        db: tools.db
        term: tools.term
        api_key: tools.api_key
      outputParameters:
      - type: object
        mapping: $.