naftiko: 1.0.0-alpha2
info:
  label: UCSC Genomic Research Workflow
  description: Workflow capability for computational biology research using the UCSC Genome Browser API. Supports genome assembly
    discovery, DNA sequence retrieval, annotation track analysis, and track hub management. Designed for bioinformaticians,
    genomics researchers, and computational biologists.
  tags:
  - Genomics
  - Bioinformatics
  - DNA Sequences
  - Annotation
  - UCSC
  - Research
  created: '2026-05-03'
  modified: '2026-05-06'
binds:
- namespace: env
  keys: {}
capability:
  consumes:
  - type: http
    namespace: ucsc-genome-browser
    baseUri: https://api.genome.ucsc.edu
    description: UCSC Genome Browser REST API — no authentication required.
    resources:
    - name: find-genome
      path: /findGenome
      description: Search for genome assemblies.
      operations:
      - name: find-genome
        method: GET
        description: Search for genomes by name, accession, or keywords.
        inputParameters:
        - name: q
          in: query
          type: string
          required: true
          description: Search query string.
        - name: maxItemsOutput
          in: query
          type: integer
          required: false
          description: Maximum number of results.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: list-ucsc-genomes
      path: /list/ucscGenomes
      description: List UCSC genome assemblies.
      operations:
      - name: list-ucsc-genomes
        method: GET
        description: Returns all genomes available in the UCSC Genome Browser.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: list-tracks
      path: /list/tracks
      description: List annotation tracks for a genome.
      operations:
      - name: list-tracks
        method: GET
        description: Returns all data tracks available for a genome assembly.
        inputParameters:
        - name: genome
          in: query
          type: string
          required: true
          description: Genome assembly identifier (e.g., hg38, mm39).
        - name: trackLeavesOnly
          in: query
          type: integer
          required: false
          description: Set to 1 to return only leaf tracks.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: list-chromosomes
      path: /list/chromosomes
      description: List chromosomes in a genome assembly.
      operations:
      - name: list-chromosomes
        method: GET
        description: Returns chromosomes and their sizes for a genome assembly.
        inputParameters:
        - name: genome
          in: query
          type: string
          required: true
          description: Genome assembly identifier (e.g., hg38, mm39).
        - name: track
          in: query
          type: string
          required: false
          description: Filter by a specific track.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: get-sequence
      path: /getData/sequence
      description: Retrieve DNA sequences.
      operations:
      - name: get-dna-sequence
        method: GET
        description: Retrieves a DNA sequence for a genomic region.
        inputParameters:
        - name: genome
          in: query
          type: string
          required: true
          description: Genome assembly identifier (e.g., hg38, mm39).
        - name: chrom
          in: query
          type: string
          required: true
          description: Chromosome identifier (e.g., chr1, chrM).
        - name: start
          in: query
          type: integer
          required: false
          description: Start position (0-based).
        - name: end
          in: query
          type: integer
          required: false
          description: End position (1-based).
        - name: revComp
          in: query
          type: integer
          required: false
          description: Set to 1 for reverse complement.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: get-track-data
      path: /getData/track
      description: Retrieve annotation track data.
      operations:
      - name: get-track-data
        method: GET
        description: Retrieves annotation data from a specific track for a genomic region.
        inputParameters:
        - name: genome
          in: query
          type: string
          required: true
          description: Genome assembly identifier (e.g., hg38, mm39).
        - name: track
          in: query
          type: string
          required: true
          description: Track name to retrieve data from.
        - name: chrom
          in: query
          type: string
          required: false
          description: Chromosome to retrieve data for.
        - name: start
          in: query
          type: integer
          required: false
          description: Start position (0-based).
        - name: end
          in: query
          type: integer
          required: false
          description: End position (1-based).
        - name: maxItemsOutput
          in: query
          type: integer
          required: false
          description: Maximum annotation items to return.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: list-public-hubs
      path: /list/publicHubs
      description: List public track hubs.
      operations:
      - name: list-public-hubs
        method: GET
        description: Returns all publicly available track hubs registered with UCSC.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: search
      path: /search
      description: Search the Genome Browser.
      operations:
      - name: search-genome-browser
        method: GET
        description: Searches track data, names, and descriptions in the Genome Browser.
        inputParameters:
        - name: search
          in: query
          type: string
          required: true
          description: Search query string.
        - name: genome
          in: query
          type: string
          required: true
          description: Genome assembly to search within.
        - name: categories
          in: query
          type: string
          required: false
          description: Restrict search scope (e.g., helpDocs, publicHubs, trackDb).
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
  exposes:
  - type: rest
    port: 8080
    namespace: ucsc-genomic-research-api
    description: Unified REST API for UCSC Genome Browser genomic data access.
    resources:
    - path: /v1/genomes
      name: genomes
      description: UCSC genome assembly listings.
      operations:
      - method: GET
        name: list-ucsc-genomes
        description: List all UCSC Genome Browser assemblies.
        call: ucsc-genome-browser.list-ucsc-genomes
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/genomes/search
      name: genome-search
      description: Genome assembly search.
      operations:
      - method: GET
        name: find-genome
        description: Search for genome assemblies by name or accession.
        call: ucsc-genome-browser.find-genome
        with:
          q: rest.q
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/genomes/{genome}/tracks
      name: tracks
      description: Annotation tracks for a genome assembly.
      operations:
      - method: GET
        name: list-tracks
        description: List all annotation tracks for a genome.
        call: ucsc-genome-browser.list-tracks
        with:
          genome: rest.genome
          trackLeavesOnly: rest.trackLeavesOnly
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/genomes/{genome}/chromosomes
      name: chromosomes
      description: Chromosome listings for a genome assembly.
      operations:
      - method: GET
        name: list-chromosomes
        description: List chromosomes and their sizes for a genome.
        call: ucsc-genome-browser.list-chromosomes
        with:
          genome: rest.genome
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/sequence
      name: sequence
      description: DNA sequence retrieval.
      operations:
      - method: GET
        name: get-dna-sequence
        description: Retrieve DNA sequence for a genomic region.
        call: ucsc-genome-browser.get-dna-sequence
        with:
          genome: rest.genome
          chrom: rest.chrom
          start: rest.start
          end: rest.end
          revComp: rest.revComp
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/track-data
      name: track-data
      description: Annotation track data retrieval.
      operations:
      - method: GET
        name: get-track-data
        description: Retrieve annotation data from a specific track for a region.
        call: ucsc-genome-browser.get-track-data
        with:
          genome: rest.genome
          track: rest.track
          chrom: rest.chrom
          start: rest.start
          end: rest.end
          maxItemsOutput: rest.maxItemsOutput
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/hubs
      name: hubs
      description: Public track hubs.
      operations:
      - method: GET
        name: list-public-hubs
        description: List all publicly available track hubs.
        call: ucsc-genome-browser.list-public-hubs
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/search
      name: search
      description: Genome Browser search.
      operations:
      - method: GET
        name: search-genome-browser
        description: Search track data, names, and descriptions in the Genome Browser.
        call: ucsc-genome-browser.search-genome-browser
        with:
          search: rest.search
          genome: rest.genome
          categories: rest.categories
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    port: 9090
    namespace: ucsc-genomic-research-mcp
    transport: http
    description: MCP server for AI-assisted genomic research using the UCSC Genome Browser.
    tools:
    - name: list-genome-assemblies
      description: List all genome assemblies available in the UCSC Genome Browser.
      hints:
        readOnly: true
        openWorld: true
      call: ucsc-genome-browser.list-ucsc-genomes
      outputParameters:
      - type: object
        mapping: $.
    - name: search-genomes
      description: Search for genome assemblies by organism name, accession, or keywords.
      hints:
        readOnly: true
        openWorld: true
      call: ucsc-genome-browser.find-genome
      with:
        q: tools.query
      outputParameters:
      - type: object
        mapping: $.
    - name: list-annotation-tracks
      description: List all annotation tracks available for a specific genome assembly.
      hints:
        readOnly: true
        openWorld: true
      call: ucsc-genome-browser.list-tracks
      with:
        genome: tools.genome
        trackLeavesOnly: tools.trackLeavesOnly
      outputParameters:
      - type: object
        mapping: $.
    - name: get-chromosomes
      description: Get chromosomes and their sizes for a genome assembly.
      hints:
        readOnly: true
        openWorld: true
      call: ucsc-genome-browser.list-chromosomes
      with:
        genome: tools.genome
      outputParameters:
      - type: object
        mapping: $.
    - name: get-dna-sequence
      description: Retrieve DNA sequence from a genome for a specified chromosomal region.
      hints:
        readOnly: true
        openWorld: true
      call: ucsc-genome-browser.get-dna-sequence
      with:
        genome: tools.genome
        chrom: tools.chrom
        start: tools.start
        end: tools.end
        revComp: tools.revComp
      outputParameters:
      - type: object
        mapping: $.
    - name: get-track-annotations
      description: Get annotation data from a specific track for a genomic region.
      hints:
        readOnly: true
        openWorld: true
      call: ucsc-genome-browser.get-track-data
      with:
        genome: tools.genome
        track: tools.track
        chrom: tools.chrom
        start: tools.start
        end: tools.end
      outputParameters:
      - type: object
        mapping: $.
    - name: list-public-track-hubs
      description: List all publicly available UCSC track hubs.
      hints:
        readOnly: true
        openWorld: true
      call: ucsc-genome-browser.list-public-hubs
      outputParameters:
      - type: object
        mapping: $.
    - name: search-genome-browser
      description: Search track data, names, and descriptions in the UCSC Genome Browser.
      hints:
        readOnly: true
        openWorld: true
      call: ucsc-genome-browser.search-genome-browser
      with:
        search: tools.query
        genome: tools.genome
        categories: tools.categories
      outputParameters:
      - type: object
        mapping: $.