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: Global cross-database query. Self-contained Naftiko
    capability covering one National Library Of Medicine business surface.'
  tags:
  - National Library Of Medicine
  - Search
  created: '2026-05-19'
  modified: '2026-05-19'
binds:
- namespace: env
  keys:
    NATIONAL_LIBRARY_OF_MEDICINE_API_KEY: NATIONAL_LIBRARY_OF_MEDICINE_API_KEY
capability:
  consumes:
  - type: http
    namespace: national-library-of-medicine-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: egquery.fcgi
      path: /egquery.fcgi
      operations:
      - name: egquery
        method: GET
        description: Global cross-database query
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: term
          in: query
          type: string
          required: true
    - name: esearch.fcgi
      path: /esearch.fcgi
      operations:
      - name: esearch
        method: GET
        description: Search a database
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: db
          in: query
          type: string
          description: Database to search (e.g. pubmed, pmc, gene, protein, nuccore).
          required: true
        - name: term
          in: query
          type: string
          description: Entrez text query, URL-encoded.
          required: true
        - name: usehistory
          in: query
          type: string
          description: Set to 'y' to post UIDs to the History server.
        - name: retmax
          in: query
          type: integer
          description: Maximum number of UIDs to return (default 20, max 10000).
        - name: retstart
          in: query
          type: integer
          description: Sequential index of the first UID to return (zero-based).
        - name: retmode
          in: query
          type: string
          description: Output format.
        - name: api_key
          in: query
          type: string
          description: NCBI API key for higher rate limits.
  exposes:
  - type: rest
    namespace: national-library-of-medicine-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/egquery-fcgi
      name: egquery-fcgi
      description: REST surface for egquery.fcgi.
      operations:
      - method: GET
        name: egquery
        description: Global cross-database query
        call: national-library-of-medicine-search.egquery
        with:
          term: rest.term
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/esearch-fcgi
      name: esearch-fcgi
      description: REST surface for esearch.fcgi.
      operations:
      - method: GET
        name: esearch
        description: Search a database
        call: national-library-of-medicine-search.esearch
        with:
          db: rest.db
          term: rest.term
          usehistory: rest.usehistory
          retmax: rest.retmax
          retstart: rest.retstart
          retmode: rest.retmode
          api_key: rest.api_key
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    namespace: national-library-of-medicine-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: global-cross-database-query
      description: Global cross-database query
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine-search.egquery
      with:
        term: tools.term
      outputParameters:
      - type: object
        mapping: $.
    - name: search-database
      description: Search a database
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine-search.esearch
      with:
        db: tools.db
        term: tools.term
        usehistory: tools.usehistory
        retmax: tools.retmax
        retstart: tools.retstart
        retmode: tools.retmode
        api_key: tools.api_key
      outputParameters:
      - type: object
        mapping: $.