Genomic Reference — Data Braids

Reference genome and gene annotation databases providing the coordinate system and functional context for all human genomics work. All braided on westGate.

RefSeq GRCh38

Human reference genome GRCh38.p14. Primary assembly plus alternate loci. The coordinate system for all human genomics — every variant, gene, and regulatory element is positioned on this assembly.

What’s Possible

• Coordinate system for variant calling and genome annotation
• Combine with NCBI Gene for variant-to-gene mapping
• Anchor for wetSpring genomic analysis pipelines
• Reference for alignment and structural variant detection

The Braid

sweetGrass braid.create produced a W3C PROV-O JSON-LD attestation:

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:refseq-grch38-westgate-20260801",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/",
    "prov:wasAssociatedWith": "did:eco:westgate"
  },
  "prov:wasAttributedTo": "did:eco:westgate",
  "prov:generatedAtTime": "2026-08-01T...",
  "eco:license": "Public Domain",
  "eco:blake3_root": "...",
  "eco:file_count": 3,
  "eco:size_bytes": 1028653056
}

NCBI Gene (Homo sapiens)

Gene information, gene2GO mappings, gene2refseq cross-references. Comprehensive gene annotation for human and model organisms. tideGlass Module 6 base data.

What’s Possible

• Gene ID resolution for cross-database linking across all datasets
• GO term enrichment for LINCS perturbation analysis
• Combine with RefSeq for variant-to-gene mapping
• Cross-reference with UniProt for protein-level annotation
• Feed tideGlass Module 6 for gene-aware pharmacology

The Braid

sweetGrass braid.create produced a W3C PROV-O JSON-LD attestation:

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:ncbi-gene-westgate-20260802",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "https://ftp.ncbi.nlm.nih.gov/gene/DATA/",
    "prov:wasAssociatedWith": "did:eco:westgate"
  },
  "prov:wasAttributedTo": "did:eco:westgate",
  "prov:generatedAtTime": "2026-08-02T...",
  "eco:license": "Public Domain",
  "eco:blake3_root": "...",
  "eco:file_count": 5,
  "eco:size_bytes": 7516192768
}

See Also

• Gene Expression — LINCS L1000, GTEx V8 (expression data)
• Proteomics — UniRef90 (protein-level cross-reference)
• Microbial Evolution — LTEE REL606 (microbial genomics)