Data repository integration for auto-fetching metadata

[jd-garv]

Automatically fetch and populate metadata from public data repositories.

Supported repositories:

• GEO (Gene Expression Omnibus)
• SRA (Sequence Read Archive)
• HCA (Human Cell Atlas)
• ArrayExpress
• Others as needed

Workflow:

1. User provides accession number (e.g., GSE12345)
2. Tool fetches metadata programmatically via API
3. Auto-populate relevant fields in datasets.md:
   • Dataset name/title
   • Data type (scRNA-seq, bulk RNA-seq, etc.)
   • Organism, tissue, cell types
   • Sample counts
   • Publication info
   • Processing level
   • Access type (Public)

Example:

User: `/biospec.fetch_dataset GSE12345`

✓ Fetched metadata for GSE12345
✓ Pre-populated Dataset 1 in datasets.md:
  - Title: Single-cell atlas of melanoma tumor microenvironment
  - Type: scRNA-seq (10X Genomics)
  - Organism: Homo sapiens
  - Tissue: Melanoma tumor
  - Samples: 48 patients
  - Publication: PMID:12345678

Benefits:

• Saves time on manual data entry
• Reduces transcription errors
• Ensures accurate metadata
• Validates data availability before analysis planning

Priority: Low / Nice to have

Note: Requires API integration with each repository