| --- |
| license: other |
| license_name: proprietary-urbankisaan |
| license_link: LICENSE |
| pretty_name: Aadi Training Data (plant genomics) |
| viewer: false |
| tags: |
| - biology |
| - genomics |
| - plant-genomics |
| - dna |
| - rna-seq |
| - atac-seq |
| - foundation-model |
| --- |
| |
| # Aadi Training Data |
|
|
| Raw and processed genomics data used to train **[Aadi](https://huggingface.co/Viharikvs/aadimodel)**, |
| a 404M-parameter plant-DNA foundation model by [UrbanKisaan Inc.](mailto:legal@urbankisaan.com) |
| This repository holds the inputs behind two stages: self-supervised pretraining of the shared |
| frozen trunk on 49 plant genomes, and supervised RNA-seq + ATAC coverage training for maize and |
| Arabidopsis. |
|
|
| > The dataset viewer is disabled on purpose. This repo contains raw sequencing reads, alignments, |
| > genome FASTA and coverage tracks (`.bam` / `.fastq.gz` / `.fa` / `.bw`), which are not tabular |
| > formats the viewer can render. Browse the files under **Files and versions** instead. |
|
|
| ## Contents |
|
|
| | Component | Size | Files | What it is | |
| |---|---|---|---| |
| | `ssl_corpus/` | 70 GB | 49 genomes | Genome FASTA for self-supervised trunk pretraining (Ensembl Plants r56; AgroNT breadth corpus + one extra) | |
| | `maize_b73_v5/` | 393 GB | ~226 | Maize (B73 NAM 5.0) RNA-seq + ATAC: raw reads, alignments, coverage, indices | |
| | `arabidopsis_tair10/` | 173 GB | ~424 | Arabidopsis (TAIR10) RNA-seq + ATAC: raw reads, alignments, coverage, indices | |
| | **Total** | **~686 GB** | **~754** | | |
|
|
| ## Directory layout |
|
|
| ``` |
| . |
| ├── ssl_corpus/ 49 plant-genome FASTAs + .fai + agront_corpus_species.txt |
| │ ├── zea_mays.fa, oryza_sativa.fa, triticum_aestivum.fa, ... |
| │ └── agront_corpus_species.txt the species manifest |
| ├── maize_b73_v5/ |
| │ ├── fastq/ raw paired-end reads (.fastq.gz) |
| │ ├── rna_bam/ STAR RNA-seq alignments (*_Aligned.sortedByCoord.out.bam + .bai) |
| │ ├── atac_bam/ bowtie2 ATAC alignments (atac_*.bam + .bai) |
| │ ├── bigwig/ per-base CPM coverage tracks (.bw) |
| │ ├── indices/ STAR / bowtie2 genome indices |
| │ ├── reference/ Zm-B73-REFERENCE-NAM-5.0 genome (.fa) + annotation (.gtf/.gff3) |
| │ ├── metadata/ sample manifests |
| │ └── logs/ alignment logs |
| └── arabidopsis_tair10/ same subfolder structure, TAIR10 |
| ``` |
|
|
| ## Provenance |
|
|
| - **SSL corpus:** 49 plant genomes from Ensembl Plants release 56 — the AgroNT 48-species breadth |
| set plus one additional genome. Species manifest: `ssl_corpus/agront_corpus_species.txt`. |
| - **Reference genomes:** |
| - Maize — `Zea_mays.Zm-B73-REFERENCE-NAM-5.0`, Ensembl Plants r61 (FASTA + GTF + GFF3). |
| - Arabidopsis — `Arabidopsis_thaliana.TAIR10`, Ensembl Plants r56 (FASTA + GTF). |
| - **Reads:** public RNA-seq and ATAC-seq runs from ENA/SRA (accessions preserved in filenames, |
| e.g. RNA `ERR2273051`, ATAC `SRR4000469`; maize ATAC `SRR28817197`, etc.). RNA aligned with |
| STAR, ATAC with bowtie2; per-base coverage computed as CPM and stored as bigWig. |
|
|
| The full acquisition and preprocessing pipeline is scripted in the Aadi repo under |
| `scripts/data_pipeline/` (`fetch_agront_corpus.sh`, `maize_align_and_bigwig.py`). |
|
|
| ## Relationship to the model |
|
|
| The frozen trunk and per-task adapters trained on this data live in |
| [`Viharikvs/aadimodel`](https://huggingface.co/Viharikvs/aadimodel). `ssl_corpus/` produced the |
| shared 404M trunk; the maize and Arabidopsis coverage data produced the supervised heads and the |
| cross-species transfer results. |
|
|
| ## License |
|
|
| Proprietary — Copyright (c) 2026 UrbanKisaan Inc. All rights reserved. The underlying genome |
| assemblies and sequencing runs are publicly available from Ensembl Plants and ENA/SRA under their |
| respective terms; the curation, processing, and assembly of this collection are proprietary. |
|
|
