omnibioai-data

Runtime data directory for the OmniBioAI platform. This repository contains the directory structure, sample files, and registry configuration needed to bootstrap a local OmniBioAI instance.

Large runtime files (datasets, uploads, results, cached data, tool images) are excluded from version control via .gitignore. The directory structure is preserved via .gitkeep files.

v0.4.0-beta — full reference genome registry (14 organisms), alignment indexes, variant databases, and AI knowledge base (35M+ PubMed abstracts, 108 FAISS indexes).

Data Scale

Category	Size
Reference genomes & indexes	~416 GB
PubMed abstracts & FAISS indexes	~195 GB
Total	~611 GB

Directory Structure

omnibioai-data/
├── datasets/               # User datasets (not tracked)
├── downloads/              # Downloaded files (not tracked)
├── uploads/                # User uploads (not tracked)
├── results/                # Analysis results (not tracked)
├── reports/                # Generated reports (not tracked)
├── logs/                   # Application logs (not tracked)
├── cache/                  # Cached data (not tracked)
├── igv_snapshots/          # IGV genome browser snapshots (not tracked)
├── single_cell/            # Single-cell analysis data (not tracked)
├── omni_object_storage/    # OmniBioAI object storage (not tracked)
├── omni_objects/           # OmniBioAI objects (not tracked)
├── objects/                # Runtime objects (not tracked)
├── reference/              # Reference genomes & annotations (not tracked)
│   ├── organisms/          # 14 organism genomes
│   ├── indexes/            # STAR, BWA, Bowtie2, Salmon, CellRanger
│   ├── variants/           # ClinVar, dbSNP, gnomAD, COSMIC
│   ├── databases/          # GO, InterPro, Pfam, UniProt
│   └── annotation/         # Ensembl, GENCODE, RefSeq, UCSC
├── PubMed/                 # AI knowledge base (not tracked)
│   ├── Abstracts/          # 35M+ PubMed abstracts (141 domains)
│   └── Index/              # FAISS vector indexes (108 domains, 8 GB)
├── scripts/                # Download and utility scripts
├── tool-images/            # Tool container images (not tracked)
├── omnibioai-tool-images/  # OmniBioAI tool images (not tracked)
├── local_registry/         # Local model/tool registry (not tracked)
├── object_registry.json    # Object registry index
├── workflow_registry.json  # Workflow registry index
└── sample files            # Sample data files for testing

Reference Genomes

14 organism genomes are stored under reference/organisms/, each at the canonical assembly version used by the platform.

Organism	Assembly
Human	GRCh37, GRCh38, T2T-CHM13
Mouse	GRCm38, GRCm39
Rat	GRCr8
Zebrafish	GRCz11
Drosophila	BDGP6
Yeast	R64
Chimpanzee	Pan_tro_3.0
Macaque	Mmul_10
C. elegans	WBcel235
Arabidopsis	TAIR10
Pig	Sscrofa11.1
Chicken	GRCg7b

Alignment Indexes

Pre-built indexes are stored under reference/indexes/.

Index	Organisms
STAR	All 14 organisms
BWA	All 14 organisms
Bowtie2	All 14 organisms
Salmon	All 14 organisms
CellRanger (2024-A)	Human only

Note: The zebrafish (GRCz11) STAR index requires ~141GB RAM to build and cannot be generated on the DGX Spark (128GB). Zebrafish RNA-seq users should use Salmon (available) or Bowtie2 (available) for alignment. The STAR index will be added post-launch when built on a higher-memory instance.

Variant Databases

Variant files are stored under reference/variants/.

Database	Build	Size
ClinVar	GRCh38	184 MB
dbSNP (latest)	GRCh38	28 GB
gnomAD v4.0 chr1	GRCh38	65 GB
COSMIC v104	GRCh37	1.1 GB
COSMIC v104	GRCh38	1.1 GB
GATK bundle (Mills + 1000G)	GRCh38	—

Note: COSMIC download requires a registered account at cancer.sanger.ac.uk. See scripts/download_cosmic.sh for the authenticated download workflow.

Functional Databases

Protein and functional annotation databases are stored under reference/databases/.

• GO — Gene Ontology
• InterPro — protein family and domain signatures
• Pfam — protein family database
• UniProt — reviewed and unreviewed protein sequences

Genome annotations (Ensembl, GENCODE, RefSeq, UCSC) are stored under reference/annotation/.

AI Knowledge Base

The PubMed/ subtree provides a local biomedical AI knowledge base for RAG-powered queries within OmniBioAI.

Component	Details
Abstracts	35M+ PubMed abstracts across 141 biomedical domains
FAISS indexes	108 domain-specific vector indexes, 8.15 GB total
Embedding model	mxbai-embed-large

Indexes are built per domain and queried at inference time by the OmniBioAI retrieval pipeline.

Scripts

Download and utility scripts are stored under scripts/.

Script	Purpose
scripts/download_cosmic.sh	Authenticated COSMIC v104 download (GRCh37 + GRCh38)
scripts/download_references.py	Reference genome downloader for all 14 organisms
scripts/download_pubmed.sh	PubMed abstracts bulk downloader

Sample Files

Small sample files are included for testing and development:

File	Description
sample1.csv	Sample expression matrix
sample2.csv	Sample expression matrix
sample1_normalize.csv	Normalized expression matrix
sample2_normalize.csv	Normalized expression matrix
sample_annotations.gff3	Sample genome annotations (GFF3)
sample_annotations.tsv	Sample annotations (TSV)
sample_regions.bed	Sample genomic regions (BED)
sample_sequences.fasta	Sample sequences (FASTA)

Setup

This directory is referenced in the OmniBioAI docker-compose stack via the DATA_DIR environment variable:

DATA_DIR=/home/manish/Desktop/machine/omnibioai-data

On first run, create the required runtime directories:

mkdir -p datasets downloads uploads results reports logs cache \
         igv_snapshots single_cell omni_object_storage omni_objects \
         objects tool-images omnibioai-tool-images local_registry \
         reference/organisms reference/indexes reference/variants \
         reference/databases reference/annotation \
         PubMed/Abstracts PubMed/Index \
         scripts

Reference Genomes

Download reference genomes for all supported organisms:

python scripts/download_references.py --all --outdir reference/organisms

To download a single organism:

python scripts/download_references.py --organism human --assembly GRCh38 \
    --outdir reference/organisms

Building Indexes

After downloading genomes, build alignment indexes:

# STAR index (example — human GRCh38)
STAR --runMode genomeGenerate \
     --genomeDir reference/indexes/star/human_GRCh38 \
     --genomeFastaFiles reference/organisms/human/GRCh38/genome.fa \
     --sjdbGTFfile reference/annotation/human/GRCh38/genes.gtf \
     --runThreadN 16

# Salmon index
salmon index \
    -t reference/organisms/human/GRCh38/transcriptome.fa \
    -i reference/indexes/salmon/human_GRCh38

COSMIC Variant Database

COSMIC requires a registered account. Set your credentials before running the download script:

export COSMIC_EMAIL="your@email.com"
export COSMIC_PASSWORD="your-password"
bash scripts/download_cosmic.sh

Related Repositories

• omnibioai — main Django workbench application
• omnibioai-tes — task execution service
• omnibioai-tool-images — tool container image definitions
• omnibioai-db-init — database initialization scripts