NCBI E-utilities API

naftiko: 1.0.0-alpha2
info:
  label: NCBI E-utilities API
  description: The Entrez Programming Utilities (E-utilities) are a public API to the NCBI Entrez system, providing access
    to all Entrez databases including PubMed, PMC, Gene, Nuccore, and Protein. The E-utilities are a suite of nine server-side
    programs that accept a fixed URL syntax for search, link, and retrieval operations. Maintained by the National Center
    for Biotechnology Information (NCBI), part of the U.S. National Library of Medicine.
  tags:
  - National
  - Library
  - Of
  - Medicine
  - API
  created: '2026-05-06'
  modified: '2026-05-06'
capability:
  consumes:
  - type: http
    namespace: national-library-of-medicine
    baseUri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils
    description: NCBI E-utilities API HTTP API.
    resources:
    - name: esearch-fcgi
      path: /esearch.fcgi
      operations:
      - name: esearch
        method: GET
        description: Search a database
        inputParameters:
        - name: db
          in: query
          type: string
          required: true
          description: Database to search (e.g. pubmed, pmc, gene, protein, nuccore).
        - name: term
          in: query
          type: string
          required: true
          description: Entrez text query, URL-encoded.
        - 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.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: efetch-fcgi
      path: /efetch.fcgi
      operations:
      - name: efetch
        method: GET
        description: Fetch full records by UID
        inputParameters:
        - name: db
          in: query
          type: string
          required: true
        - name: id
          in: query
          type: string
          required: true
          description: Comma-separated list of UIDs or a WebEnv/query_key reference.
        - name: rettype
          in: query
          type: string
          description: Retrieval type (e.g. abstract, fasta, gb, medline).
        - name: retmode
          in: query
          type: string
          description: Retrieval mode (e.g. xml, text, json, asn.1).
        - name: api_key
          in: query
          type: string
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: esummary-fcgi
      path: /esummary.fcgi
      operations:
      - name: esummary
        method: GET
        description: Retrieve document summaries
        inputParameters:
        - name: db
          in: query
          type: string
          required: true
        - name: id
          in: query
          type: string
          required: true
        - name: version
          in: query
          type: string
          description: Set to '2.0' for the newer DocSum schema.
        - name: retmode
          in: query
          type: string
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: einfo-fcgi
      path: /einfo.fcgi
      operations:
      - name: einfo
        method: GET
        description: Database statistics and field metadata
        inputParameters:
        - name: db
          in: query
          type: string
        - name: retmode
          in: query
          type: string
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: elink-fcgi
      path: /elink.fcgi
      operations:
      - name: elink
        method: GET
        description: Find related records across Entrez databases
        inputParameters:
        - name: dbfrom
          in: query
          type: string
          required: true
        - name: db
          in: query
          type: string
        - name: id
          in: query
          type: string
          required: true
        - name: linkname
          in: query
          type: string
        - name: cmd
          in: query
          type: string
          description: Command mode (neighbor, neighbor_history, llinks, prlinks, etc.).
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: epost-fcgi
      path: /epost.fcgi
      operations:
      - name: epost
        method: POST
        description: Post UIDs to the Entrez History server
        inputParameters:
        - name: db
          in: query
          type: string
          required: true
        - name: id
          in: query
          type: string
          required: true
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: espell-fcgi
      path: /espell.fcgi
      operations:
      - name: espell
        method: GET
        description: Spelling suggestions for a query term
        inputParameters:
        - name: db
          in: query
          type: string
          required: true
        - name: term
          in: query
          type: string
          required: true
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: ecitmatch-cgi
      path: /ecitmatch.cgi
      operations:
      - name: ecitmatch
        method: GET
        description: Match citations to PubMed UIDs
        inputParameters:
        - name: db
          in: query
          type: string
          required: true
        - name: rettype
          in: query
          type: string
        - name: bdata
          in: query
          type: string
          required: true
          description: Pipe-delimited citation strings.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: egquery-fcgi
      path: /egquery.fcgi
      operations:
      - name: egquery
        method: GET
        description: Global cross-database query
        inputParameters:
        - name: term
          in: query
          type: string
          required: true
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
  exposes:
  - type: rest
    port: 8080
    namespace: national-library-of-medicine-rest
    description: REST adapter for NCBI E-utilities API.
    resources:
    - path: /esearch.fcgi
      name: esearch
      operations:
      - method: GET
        name: esearch
        description: Search a database
        call: national-library-of-medicine.esearch
        outputParameters:
        - type: object
          mapping: $.
    - path: /efetch.fcgi
      name: efetch
      operations:
      - method: GET
        name: efetch
        description: Fetch full records by UID
        call: national-library-of-medicine.efetch
        outputParameters:
        - type: object
          mapping: $.
    - path: /esummary.fcgi
      name: esummary
      operations:
      - method: GET
        name: esummary
        description: Retrieve document summaries
        call: national-library-of-medicine.esummary
        outputParameters:
        - type: object
          mapping: $.
    - path: /einfo.fcgi
      name: einfo
      operations:
      - method: GET
        name: einfo
        description: Database statistics and field metadata
        call: national-library-of-medicine.einfo
        outputParameters:
        - type: object
          mapping: $.
    - path: /elink.fcgi
      name: elink
      operations:
      - method: GET
        name: elink
        description: Find related records across Entrez databases
        call: national-library-of-medicine.elink
        outputParameters:
        - type: object
          mapping: $.
    - path: /epost.fcgi
      name: epost
      operations:
      - method: POST
        name: epost
        description: Post UIDs to the Entrez History server
        call: national-library-of-medicine.epost
        outputParameters:
        - type: object
          mapping: $.
    - path: /espell.fcgi
      name: espell
      operations:
      - method: GET
        name: espell
        description: Spelling suggestions for a query term
        call: national-library-of-medicine.espell
        outputParameters:
        - type: object
          mapping: $.
    - path: /ecitmatch.cgi
      name: ecitmatch
      operations:
      - method: GET
        name: ecitmatch
        description: Match citations to PubMed UIDs
        call: national-library-of-medicine.ecitmatch
        outputParameters:
        - type: object
          mapping: $.
    - path: /egquery.fcgi
      name: egquery
      operations:
      - method: GET
        name: egquery
        description: Global cross-database query
        call: national-library-of-medicine.egquery
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    port: 9090
    namespace: national-library-of-medicine-mcp
    transport: http
    description: MCP adapter for NCBI E-utilities API for AI agent use.
    tools:
    - name: esearch
      description: Search a database
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine.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
      inputParameters:
      - name: db
        type: string
        description: Database to search (e.g. pubmed, pmc, gene, protein, nuccore).
        required: true
      - name: term
        type: string
        description: Entrez text query, URL-encoded.
        required: true
      - name: usehistory
        type: string
        description: Set to 'y' to post UIDs to the History server.
      - name: retmax
        type: integer
        description: Maximum number of UIDs to return (default 20, max 10000).
      - name: retstart
        type: integer
        description: Sequential index of the first UID to return (zero-based).
      - name: retmode
        type: string
        description: Output format.
      - name: api_key
        type: string
        description: NCBI API key for higher rate limits.
      outputParameters:
      - type: object
        mapping: $.
    - name: efetch
      description: Fetch full records by UID
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine.efetch
      with:
        db: tools.db
        id: tools.id
        rettype: tools.rettype
        retmode: tools.retmode
        api_key: tools.api_key
      inputParameters:
      - name: db
        type: string
        description: db
        required: true
      - name: id
        type: string
        description: Comma-separated list of UIDs or a WebEnv/query_key reference.
        required: true
      - name: rettype
        type: string
        description: Retrieval type (e.g. abstract, fasta, gb, medline).
      - name: retmode
        type: string
        description: Retrieval mode (e.g. xml, text, json, asn.1).
      - name: api_key
        type: string
        description: api_key
      outputParameters:
      - type: object
        mapping: $.
    - name: esummary
      description: Retrieve document summaries
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine.esummary
      with:
        db: tools.db
        id: tools.id
        version: tools.version
        retmode: tools.retmode
      inputParameters:
      - name: db
        type: string
        description: db
        required: true
      - name: id
        type: string
        description: id
        required: true
      - name: version
        type: string
        description: Set to '2.0' for the newer DocSum schema.
      - name: retmode
        type: string
        description: retmode
      outputParameters:
      - type: object
        mapping: $.
    - name: einfo
      description: Database statistics and field metadata
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine.einfo
      with:
        db: tools.db
        retmode: tools.retmode
      inputParameters:
      - name: db
        type: string
        description: db
      - name: retmode
        type: string
        description: retmode
      outputParameters:
      - type: object
        mapping: $.
    - name: elink
      description: Find related records across Entrez databases
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine.elink
      with:
        dbfrom: tools.dbfrom
        db: tools.db
        id: tools.id
        linkname: tools.linkname
        cmd: tools.cmd
      inputParameters:
      - name: dbfrom
        type: string
        description: dbfrom
        required: true
      - name: db
        type: string
        description: db
      - name: id
        type: string
        description: id
        required: true
      - name: linkname
        type: string
        description: linkname
      - name: cmd
        type: string
        description: Command mode (neighbor, neighbor_history, llinks, prlinks, etc.).
      outputParameters:
      - type: object
        mapping: $.
    - name: epost
      description: Post UIDs to the Entrez History server
      hints:
        readOnly: false
        destructive: false
        idempotent: false
      call: national-library-of-medicine.epost
      with:
        db: tools.db
        id: tools.id
      inputParameters:
      - name: db
        type: string
        description: db
        required: true
      - name: id
        type: string
        description: id
        required: true
      outputParameters:
      - type: object
        mapping: $.
    - name: espell
      description: Spelling suggestions for a query term
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine.espell
      with:
        db: tools.db
        term: tools.term
      inputParameters:
      - name: db
        type: string
        description: db
        required: true
      - name: term
        type: string
        description: term
        required: true
      outputParameters:
      - type: object
        mapping: $.
    - name: ecitmatch
      description: Match citations to PubMed UIDs
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine.ecitmatch
      with:
        db: tools.db
        rettype: tools.rettype
        bdata: tools.bdata
      inputParameters:
      - name: db
        type: string
        description: db
        required: true
      - name: rettype
        type: string
        description: rettype
      - name: bdata
        type: string
        description: Pipe-delimited citation strings.
        required: true
      outputParameters:
      - type: object
        mapping: $.
    - name: egquery
      description: Global cross-database query
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-library-of-medicine.egquery
      with:
        term: tools.term
      inputParameters:
      - name: term
        type: string
        description: term
        required: true
      outputParameters:
      - type: object
        mapping: $.