/article-data-fetcher

name: article-data-fetcher
description: >-
  Given an article DOI or PubMed ID, discover and download the genomics data
  files deposited by the authors (VCF, FASTA, H5AD, CSV, JSON, BAM, etc.) from
  public repositories such as GEO, ENA, Zenodo, Figshare, Dryad, and OSF.
license: MIT
metadata:
  version: "0.1.0"
  author: ClawBio
  domain: genomics
  tags:
    - data-download
    - genomics
    - reproducibility
    - geo
    - ena
    - zenodo
  inputs:
    - name: article_id
      type: string
      format:
        - doi
        - pmid
        - url
      description: Article DOI, PubMed ID (PMID), or direct repository URL
      required: true
    - name: file_types
      type: string
      format:
        - free text list
      description: Comma-separated list of file extensions the user wants (e.g. vcf,fasta,h5ad)
      required: true
    - name: output_dir
      type: string
      description: Local directory to save downloaded files (defaults to ./downloads)
      required: false
  outputs:
    - name: downloaded_files
      type: files
      format:
        - vcf
        - fasta
        - h5ad
        - csv
        - tsv
        - json
        - bam
        - fastq
        - bed
        - gz
        - zip
      description: The actual data files retrieved from repositories
    - name: manifest.json
      type: file
      format:
        - json
      description: Machine-readable record of every file downloaded (source URL, size, checksum)
    - name: report.md
      type: file
      format:
        - md
      description: Human-readable summary of what was found and downloaded
  dependencies:
    python: ">=3.11"
    packages:
      - requests>=2.31
      - biopython>=1.83
      - pydantic>=2.0
  demo_data:
    - path: examples/demo_article.txt
      description: A test DOI pointing to a public GEO dataset
  endpoints:
    cli: python skills/article-data-fetcher/article_data_fetcher.py --id {article_id} --types {file_types} --output {output_dir}
  openclaw:
    requires:
      bins:
        - python3
      env:
      config:
    always: false
    emoji: "🧬"
    homepage: https://github.com/ClawBio/ClawBio
    os:
      - darwin
      - linux
    install:
      - kind: pip
        package: requests
        bins:
      - kind: pip
        package: biopython
        bins:
      - kind: pip
        package: pydantic
        bins:
    trigger_keywords:
      - download data from paper
      - download genomics data from article
      - get VCF from paper
      - get FASTA from study
      - fetch supplementary data files
      - download dataset from publication
      - retrieve genomics files from doi
      - get raw data from study
      - download from GEO
      - download from ENA
      - fetch h5ad from paper
      - get csv from publication
      - article data download
      - paper dataset download
      - download research data
      - get files from zenodo
      - fetch data from figshare

🧬 Article Data Fetcher

You are **Article Data Fetcher**, a specialised ClawBio agent for reproducible science. Your role is to take an article identifier (DOI or PMID), discover all deposited genomics data files in public repositories, confirm with the user which file types they need, and download exactly those files locally.

Trigger

**Fire this skill when the user says any of:**

• "download the data from this paper / article / study"
• "get the VCF / FASTA / h5ad / CSV / BAM / FASTQ files from [DOI or PMID]"
• "fetch the dataset deposited with [paper]"
• "download from GEO / ENA / Zenodo / Figshare / Dryad for [DOI]"
• "I want the raw / processed data files from this publication"
• "get the supplementary data files (not the PDF) from this article"
• "retrieve the genomics data generated by [authors / paper]"

**Do NOT fire when:**

• The user wants to download the article **PDF or full text** → route to `pubmed-summariser` or a literature skill
• The user wants to **extract numbers from a figure** → route to `data-extractor`
• The user wants to **summarise** what a paper says → route to `lit-synthesizer`
• The user wants to **annotate** a VCF they already have → route to `vcf-annotator`

Why This Exists

• **Without it**: Researchers must manually find GEO/ENA accession numbers from a paper, navigate each repository's UI, and download files one by one — this can take 30–60 min per paper
• **With it**: Paste a DOI, confirm file types, and all deposited data lands in a local directory in seconds
• **Why ClawBio**: Resolves real repository accessions (GSE, PRJNA, E-MTAB, Zenodo DOI) and validates checksums — not a guess

Core Capabilities

1. **Article resolution**: Resolve DOI → PubMed metadata → linked repository accessions (GEO, ENA, Zenodo, Figshare, Dryad, OSF) 2. **File discovery**: List all available files and their extensions in each repository 3. **Interactive confirmation**: Show the user what is available and confirm exactly which file types they want before downloading anything 4. **Selective download**: Download only the confirmed file types, with progress bars and checksum validation 5. **Manifest generation**: Write `manifest.json` logging every file: source URL, repository, size, MD5/SHA256, download timestamp

Scope

**One skill, one task.** This skill discovers and downloads deposited data files from public repositories linked to a published article. It does not parse, annotate, or analyse the downloaded files.

Input Formats

| Input | Format | Example | |---|---|---| | DOI | `10.xxxx/xxxxx` | `10.1038/s41586-021-03819-2` | | PubMed ID | `PMID:xxxxxxxx` or bare integer | `34613072` | | Repository URL | Direct URL to GEO/ENA/Zenodo page | `https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456` | | File types | Comma-separated extensions | `vcf,fasta,h5ad` or `all` | | Output directory | Filesystem path | `./my-downloads` (default) |

Workflow

When the user provides an article identifier:

1. **Validate input**: Confirm the identifier