InstaDeepAI/NTv3_benchmark_dataset

NTv3 Benchmark Dataset

This dataset contains the functional tracks and genome annotations used in the NTv3 benchmark evaluation.

Dataset Organization

The dataset is organized as follows:

InstaDeepAI/NTv3_benchmark_dataset/
├── <species>/
│   ├── functional_tracks/
│   │   ├── <track_name>.bigwig
│   │   └── ...
│   └── genome_annotation/
│       ├── <track_name>.bed
│       └── ...

Available Species

• arabidopsis
• chicken
• cattle
• human
• maize
• rice
• tomato

Downloading Files

You can download files directly using their URLs:

from huggingface_hub import hf_hub_download
import requests

# Download a BigWig file
bigwig_path = hf_hub_download(
    repo_id="InstaDeepAI/NTv3_benchmark_dataset",
    filename="human/functional_tracks/ENCSR628PLS.bigwig",
    repo_type="dataset"
)

# Download a BED file
bed_path = hf_hub_download(
    repo_id="InstaDeepAI/NTv3_benchmark_dataset",
    filename="human/genome_annotation/exon.bed",
    repo_type="dataset"
)

Direct URL Access

You can also construct direct URLs to download files:

import requests

# Construct URL
base_url = 'https://huggingface.co/datasets/InstaDeepAI/NTv3_benchmark_dataset/resolve/main'
file_path = "human/functional_tracks/ENCSR628PLS.bigwig"
url = f"{base_url}/{file_path}"

# Download file
response = requests.get(url)
with open("local_file.bigwig", "wb") as f:
    f.write(response.content)

Available Tracks

Human

Functional Tracks

Files are named by their S3 track ID (file_id). The mapping from track ID to track description can be found in the benchmark documentation.

• human/functional_tracks/ENCSR628PLS.bigwig (GM18861_chromatin_accessibility)
• human/functional_tracks/ENCSR487QSB.bigwig (GM18907_chromatin_accessibility)
• human/functional_tracks/ENCSR410DWV.bigwig (motor_neuron_chromatin_accessibility)
• human/functional_tracks/ENCSR325NFE.bigwig (bile_duct_chromatin_accessibility)
• human/functional_tracks/ENCSR814RGG.bigwig (ureter_chromatin_accessibility)
• human/functional_tracks/ENCSR863PSM.bigwig (BLaER1_H3K4me1)
• human/functional_tracks/ENCSR682BFG.bigwig (motor_neuron_H3K4me1)
• human/functional_tracks/ENCSR754DRC.bigwig (motor_neuron_H3K27ac)
• human/functional_tracks/ENCSR962OTG.bigwig (motor_neuron_H3K4me3)
• human/functional_tracks/ENCSR046BCI_M.bigwig (A673_PROcap_minus)
• human/functional_tracks/ENCSR046BCI_P.bigwig (A673_PROcap_plus)
• human/functional_tracks/ENCSR100LIJ_M.bigwig (Caco-2_PROcap_minus)
• human/functional_tracks/ENCSR100LIJ_P.bigwig (Caco-2_PROcap_plus)
• human/functional_tracks/ENCSR935RNW_M.bigwig (Calu3_PROcap_minus)
• human/functional_tracks/ENCSR935RNW_P.bigwig (Calu3_PROcap_plus)
• human/functional_tracks/ENCSR114HGS_M.bigwig (K562_PROcap_minus)
• human/functional_tracks/ENCSR114HGS_P.bigwig (K562_PROcap_plus)
• human/functional_tracks/ENCSR799DGV_M.bigwig (MCF10A_PROcap_minus)
• human/functional_tracks/ENCSR799DGV_P.bigwig (MCF10A_PROcap_plus)
• human/functional_tracks/ENCSR154HRN_M.bigwig (K562_HNRNPA1_eCLIP_minus)
• human/functional_tracks/ENCSR154HRN_P.bigwig (K562_HNRNPA1_eCLIP_plus)
• human/functional_tracks/ENCSR249ROI_M.bigwig (K562_HNRNPC_eCLIP_minus)
• human/functional_tracks/ENCSR249ROI_P.bigwig (K562_HNRNPC_eCLIP_plus)
• human/functional_tracks/ENCSR321PWZ_M.bigwig (K562_SRSF1_eCLIP_minus)
• human/functional_tracks/ENCSR321PWZ_P.bigwig (K562_SRSF1_eCLIP_plus)
• human/functional_tracks/ENCSR484LTQ_M.bigwig (K562_NCBP2_eCLIP_minus)
• human/functional_tracks/ENCSR484LTQ_P.bigwig (K562_NCBP2_eCLIP_plus)
• human/functional_tracks/ENCSR862QCH_M.bigwig (K562_U2AF1_eCLIP_minus)
• human/functional_tracks/ENCSR862QCH_P.bigwig (K562_U2AF1_eCLIP_plus)
• human/functional_tracks/ENCSR527JGN_M.bigwig (BLaER1_gene_expression_minus)
• human/functional_tracks/ENCSR527JGN_P.bigwig (BLaER1_gene_expression_plus)
• human/functional_tracks/ENCSR701YIC.bigwig (motor_neuron_gene_expression)
• human/functional_tracks/ENCSR619DQO_M.bigwig (ureter_gene_expression_minus)
• human/functional_tracks/ENCSR619DQO_P.bigwig (ureter_gene_expression_plus)

Genome Annotations

• human/genome_annotation/exon.bed (exon)
• human/genome_annotation/intron.bed (intron)
• human/genome_annotation/splice_acceptor.bed (splice_acceptor)
• human/genome_annotation/start_codon.bed (start_codon)

Chicken

Functional Tracks

• chicken/functional_tracks/ERX9662174.bigwig (bone_marrow_chromatin_accessibility)
• chicken/functional_tracks/ERX9662188.bigwig (bone_marrow_gene_expression)
• chicken/functional_tracks/ERX9662177.bigwig (heart_chromatin_accessibility)
• chicken/functional_tracks/ERX9662190.bigwig (heart_gene_expression)
• chicken/functional_tracks/ERX9662178.bigwig (kidney_chromatin_accessibility)
• chicken/functional_tracks/ERX9662192.bigwig (kidney_gene_expression)
• chicken/functional_tracks/ERX9662183.bigwig (testis_chromatin_accessibility)
• chicken/functional_tracks/ERX9662196.bigwig (testis_gene_expression)
• chicken/functional_tracks/ERX9662185.bigwig (thymus_chromatin_accessibility)
• chicken/functional_tracks/ERX9662198.bigwig (thymus_gene_expression)
• chicken/functional_tracks/ERX9662186.bigwig (trachea_chromatin_accessibility)
• chicken/functional_tracks/ERX9662200.bigwig (trachea_gene_expression)
• chicken/functional_tracks/ERX9662180.bigwig (uterus_chromatin_accessibility)
• chicken/functional_tracks/ERX9662194.bigwig (uterus_gene_expression)

Arabidopsis

Functional Tracks

• arabidopsis/functional_tracks/SRR13808079.bigwig (flower_mature_riboseq)
• arabidopsis/functional_tracks/SRR13808080.bigwig (flower_mature_riboseq_2)
• arabidopsis/functional_tracks/SRR13808081.bigwig (fruit_mature_riboseq)
• arabidopsis/functional_tracks/SRR13808084.bigwig (root_mature_riboseq)

Rice

Functional Tracks

• rice/functional_tracks/SRR13808064.bigwig (leaf_V2_stage_riboseq)
• rice/functional_tracks/SRR13808065.bigwig (leaf_V2_stage_riboseq_2)
• rice/functional_tracks/SRR13808066.bigwig (leaf_booting_stage_riboseq_2)
• rice/functional_tracks/SRR13808067.bigwig (leaf_booting_stage_riboseq)
• rice/functional_tracks/SRR13808068.bigwig (root_V2_stage_riboseq)
• rice/functional_tracks/SRR13808069.bigwig (seedling_V2_stage_riboseq)
• rice/functional_tracks/SRR13808070.bigwig (sheath_V2_stage_riboseq)
• rice/functional_tracks/SRR13808072.bigwig (sheath_V2_stage_riboseq_2)
• rice/functional_tracks/SRR13808073.bigwig (sheath_booting_stage_riboseq)
• rice/functional_tracks/SRR13808074.bigwig (sheath_booting_stage_riboseq_2)
• rice/functional_tracks/SRR13808075.bigwig (spikelet_booting_stage_riboseq)
• rice/functional_tracks/SRR13808076.bigwig (spikelet_booting_stage_riboseq_2)
• rice/functional_tracks/SRR13808077.bigwig (stem_booting_stage_riboseq)
• rice/functional_tracks/SRR13808078.bigwig (stem_booting_stage_riboseq_2)

Maize

Functional Tracks

• maize/functional_tracks/SRR13808051.bigwig (ear_V12_stage_riboseq)
• maize/functional_tracks/SRR13808052.bigwig (ear_V12_stage_riboseq_2)
• maize/functional_tracks/SRR13808056.bigwig (root_14days_riboseq)
• maize/functional_tracks/SRR13808058.bigwig (seedling_14days_riboseq)
• maize/functional_tracks/SRR13808059.bigwig (stem_14days_riboseq)
• maize/functional_tracks/SRR13808061.bigwig (stem_14days_riboseq_2)
• maize/functional_tracks/SRR13808062.bigwig (tassel_V12_stage_riboseq)
• maize/functional_tracks/SRR13808063.bigwig (tassel_V12_stage_riboseq_2)

Tomato

Functional Tracks

• tomato/functional_tracks/SRX27799703.bigwig (fruit_0DPA_chromatin_accessibility)
• tomato/functional_tracks/SRX29291440.bigwig (fruit_0DPA_MicroTom_gene_expression)
• tomato/functional_tracks/SRX29291439.bigwig (fruit_0DPA_MicroTom_gene_expression_2)
• tomato/functional_tracks/SRX29291438.bigwig (fruit_0DPA_MicroTom_gene_expression_3)
• tomato/functional_tracks/SRX27799731.bigwig (fruit_10DPA_chromatin_accessibility)
• tomato/functional_tracks/SRX29291448.bigwig (fruit_10DPA_MicroTom_gene_expression)
• tomato/functional_tracks/SRX29291447.bigwig (fruit_10DPA_MicroTom_gene_expression_2)
• tomato/functional_tracks/SRX29291446.bigwig (fruit_10DPA_MicroTom_gene_expression_3)
• tomato/functional_tracks/SRX29291431.bigwig (fruit_15DPA_MicroTom_gene_expression)
• tomato/functional_tracks/SRX29291430.bigwig (fruit_15DPA_MicroTom_gene_expression_2)
• tomato/functional_tracks/SRX29291445.bigwig (fruit_15DPA_Wild_LA1781_gene_expression)
• tomato/functional_tracks/SRX29291442.bigwig (fruit_15DPA_Wild_LA1781_gene_expression_2)
• tomato/functional_tracks/SRX27799722.bigwig (fruit_3DBA_chromatin_accessibility)
• tomato/functional_tracks/SRX27799719.bigwig (fruit_3DPA_chromatin_accessibility)
• tomato/functional_tracks/SRX27799727.bigwig (fruit_5DPA_chromatin_accessibility)
• tomato/functional_tracks/SRX29291444.bigwig (fruit_5DPA_MicroTom_gene_expression)
• tomato/functional_tracks/SRX29291443.bigwig (fruit_5DPA_MicroTom_gene_expression_2)
• tomato/functional_tracks/SRX29291441.bigwig (fruit_5DPA_MicroTom_gene_expression_3)
• tomato/functional_tracks/SRX27799718.bigwig (fruit_7DPA_chromatin_accessibility)
• tomato/functional_tracks/SRX27799733.bigwig (leaf_chromatin_accessibility)

Genome Annotations

• tomato/genome_annotation/exon.bed (exon)
• tomato/genome_annotation/intron.bed (intron)
• tomato/genome_annotation/splice_acceptor.bed (splice_acceptor)
• tomato/genome_annotation/start_codon.bed (start_codon)

Cattle

Genome Annotations

• cattle/genome_annotation/exon.bed (exon)
• cattle/genome_annotation/intron.bed (intron)
• cattle/genome_annotation/splice_acceptor.bed (splice_acceptor)
• cattle/genome_annotation/start_codon.bed (start_codon)

Track Information

Functional Tracks

Functional tracks include:

• Chromatin Accessibility tracks
• Histone modifications (H3K4me1, H3K4me3, H3K27ac)
• Transcription initiation (PRO-cap)
• RNA binding sites (eCLIP)
• Gene Expression
• mRNA translation (Ribo-seq)

Genome Annotations

Genome annotation tracks include:

• Exon
• Intron
• Splice Acceptor
• Start Codon

Notes

• BigWig files can be read using libraries like pyBigWig
• BED files can be read using pyranges or pandas
• All tracks are in the same coordinate system as specified in the benchmark