Datasets:

InstaDeepAI
/

NTv3_benchmark_dataset_revised

language:
  - en
pretty_name: NTv3 benchmark dataset (revised) - Genomes & functional tracks
tags:
  - 🧬 genomics
  - 📊 bigwig / functional tracks
  - 🎯 regression
  - ⚡ fine-tuning
  - 🧪 sequence-to-signal
  - 📐 functional-genomics
  - 🔬 bioinformatics
task_categories:
  - other
size_categories:
  - n<1K
license: cc-by-nc-4.0

NTv3 Benchmark Dataset (revised)

Genomes, train/val/test splits and functional tracks (BigWig) of the revised NTv3 benchmark: 155 tracks over 11 species. The benchmark fine-tunes a model to predict every track of a species from its DNA sequence, and reports the mean Pearson correlation over the tracks of the test regions.

Dataset organization

InstaDeepAI/NTv3_benchmark_dataset_revised/
├── benchmark_metadata.tsv          # one row per track
└── <species>/
    ├── genome.fasta                # one record per chromosome
    ├── splits.bed                  # train / val / test regions
    └── functional_tracks/
        └── <file_id>.bigwig

Species

Directory	Species	Scientific name	Assembly	Tracks	Assays
`arabidopsis`	Arabidopsis	Arabidopsis thaliana	TAIR10	4	ribo-seq (4)
`human`	Human	Homo sapiens	hg38	34	PRO-cap (10), eCLIP (10), ATAC-seq (5), Histone ChIP-seq (4), total RNA-seq (3), polyA plus RNA-seq (2)
`maize`	Maize	Zea mays	Zm-B73-REFERENCE-NAM-5.0	8	ribo-seq (8)
`rice`	Rice	Oryza sativa	IRGSP-1.0	14	ribo-seq (14)
`tomato`	Tomato	Solanum lycopersicum	SL3	20	RNA-seq (13), ATAC-seq (7)
`cattle`	Cattle	Bos taurus	ARS-UCD1.2	30	Histone ChIP-seq (12), ATAC-seq (7), TF ChIP-seq (6), RNA-seq (5)
`fission_yeast`	Fission yeast	Schizosaccharomyces pombe	ASM294v2	7	ATAC-seq (5), RNA-seq (2)
`malaria_parasite`	Malaria parasite	Plasmodium falciparum	GCA000002765v3	7	ATAC-seq (4), RNA-seq (3)
`rat`	Rat	Rattus norvegicus	mRatBN7	12	RNA-seq (9), ATAC-seq (3)
`soil_amoeba`	Soil amoeba	Dictyostelium discoideum	dicty_2.7	7	RNA-seq (7)
`yeast`	Yeast	Saccharomyces cerevisiae	R64	12	RNA-seq (7), ATAC-seq (5)

Files

genome.fasta: the reference genome. Record names match the chromosome names of splits.bed and of the BigWig files.
splits.bed: tab-separated, no header, columns chrom, start, end, split (train, val or test), 0-based half-open. The regions do not overlap, and each one belongs to a single split.
functional_tracks/<file_id>.bigwig: per-base signal, read with pyBigWig.
benchmark_metadata.tsv: one row per track, with columns
- file_id: name of the BigWig file,
- species_common_name: the species directory,
- species_name, file_assembly,
- mean, std: genome-wide statistics of the track,
- assay: experiment type,
- description: biosample and assay of the track.

Target scaling used in the benchmark

Targets are divided by the track's genome-wide mean, tracks whose assay contains RNA-seq are raised to the power 0.75, and values above 10 are soft-clipped. Input sequences are upper-cased and any character outside ACGTN is replaced by N.

Download

from huggingface_hub import hf_hub_download, snapshot_download

# One file
bigwig_path = hf_hub_download(
    repo_id="InstaDeepAI/NTv3_benchmark_dataset_revised",
    filename="cattle/functional_tracks/ERR1464183.bigwig",
    repo_type="dataset",
)

# One species
local_dir = snapshot_download(
    repo_id="InstaDeepAI/NTv3_benchmark_dataset_revised",
    repo_type="dataset",
    allow_patterns=["benchmark_metadata.tsv", "yeast/*"],
)

Tracks

Arabidopsis (`arabidopsis`, TAIR10)

file_id	assay	description
`SRR13808079`	ribo-seq	flower_mature_riboseq
`SRR13808080`	ribo-seq	flower_mature_riboseq_2
`SRR13808081`	ribo-seq	fruit_mature_riboseq
`SRR13808084`	ribo-seq	root_mature_riboseq

Human (`human`, hg38)

file_id	assay	description
`ENCSR628PLS`	ATAC-seq	GM18861_chromatin_accessibility
`ENCSR487QSB`	ATAC-seq	GM18907_chromatin_accessibility
`ENCSR410DWV`	ATAC-seq	motor_neuron_chromatin_accessibility
`ENCSR325NFE`	ATAC-seq	bile_duct_chromatin_accessibility
`ENCSR814RGG`	ATAC-seq	ureter_chromatin_accessibility
`ENCSR863PSM`	Histone ChIP-seq	BLaER1_H3K4me1
`ENCSR682BFG`	Histone ChIP-seq	motor_neuron_H3K4me1
`ENCSR754DRC`	Histone ChIP-seq	motor_neuron_H3K27ac
`ENCSR962OTG`	Histone ChIP-seq	motor_neuron_H3K4me3
`ENCSR046BCI_M`	PRO-cap	A673_PROcap_minus
`ENCSR046BCI_P`	PRO-cap	A673_PROcap_plus
`ENCSR100LIJ_M`	PRO-cap	Caco-2_PROcap_minus
`ENCSR100LIJ_P`	PRO-cap	Caco-2_PROcap_plus
`ENCSR935RNW_M`	PRO-cap	Calu3_PROcap_minus
`ENCSR935RNW_P`	PRO-cap	Calu3_PROcap_plus
`ENCSR114HGS_M`	PRO-cap	K562_PROcap_minus
`ENCSR114HGS_P`	PRO-cap	K562_PROcap_plus
`ENCSR799DGV_M`	PRO-cap	MCF10A_PROcap_minus
`ENCSR799DGV_P`	PRO-cap	MCF10A_PROcap_plus
`ENCSR154HRN_M`	eCLIP	K562_HNRNPA1_eCLIP_minus
`ENCSR154HRN_P`	eCLIP	K562_HNRNPA1_eCLIP_plus
`ENCSR249ROI_M`	eCLIP	K562_HNRNPC_eCLIP_minus
`ENCSR249ROI_P`	eCLIP	K562_HNRNPC_eCLIP_plus
`ENCSR321PWZ_M`	eCLIP	K562_SRSF1_eCLIP_minus
`ENCSR321PWZ_P`	eCLIP	K562_SRSF1_eCLIP_plus
`ENCSR484LTQ_M`	eCLIP	K562_NCBP2_eCLIP_minus
`ENCSR484LTQ_P`	eCLIP	K562_NCBP2_eCLIP_plus
`ENCSR862QCH_M`	eCLIP	K562_U2AF1_eCLIP_minus
`ENCSR862QCH_P`	eCLIP	K562_U2AF1_eCLIP_plus
`ENCSR527JGN_M`	polyA plus RNA-seq	BLaER1_gene_expression_minus
`ENCSR527JGN_P`	polyA plus RNA-seq	BLaER1_gene_expression_plus
`ENCSR701YIC`	total RNA-seq	motor_neuron_gene_expression
`ENCSR619DQO_M`	total RNA-seq	ureter_gene_expression_minus
`ENCSR619DQO_P`	total RNA-seq	ureter_gene_expression_plus

Maize (`maize`, Zm-B73-REFERENCE-NAM-5.0)

file_id	assay	description
`SRR13808051`	ribo-seq	ear_V12_stage_riboseq
`SRR13808052`	ribo-seq	ear_V12_stage_riboseq_2
`SRR13808056`	ribo-seq	root_14days_riboseq
`SRR13808058`	ribo-seq	seedling_14days_riboseq
`SRR13808059`	ribo-seq	stem_14days_riboseq
`SRR13808061`	ribo-seq	stem_14days_riboseq_2
`SRR13808062`	ribo-seq	tassel_V12_stage_riboseq
`SRR13808063`	ribo-seq	tassel_V12_stage_riboseq_2

Rice (`rice`, IRGSP-1.0)

file_id	assay	description
`SRR13808067`	ribo-seq	leaf_booting_stage_riboseq
`SRR13808068`	ribo-seq	root_V2_stage_riboseq
`SRR13808069`	ribo-seq	seedling_V2_stage_riboseq
`SRR13808070`	ribo-seq	sheath_V2_stage_riboseq
`SRR13808072`	ribo-seq	sheath_V2_stage_riboseq_2
`SRR13808073`	ribo-seq	sheath_booting_stage_riboseq
`SRR13808074`	ribo-seq	sheath_booting_stage_riboseq_2
`SRR13808075`	ribo-seq	spikelet_booting_stage_riboseq
`SRR13808076`	ribo-seq	spikelet_booting_stage_riboseq_2
`SRR13808077`	ribo-seq	stem_booting_stage_riboseq
`SRR13808078`	ribo-seq	stem_booting_stage_riboseq_2
`SRR13808064`	ribo-seq	leaf_V2_stage_riboseq
`SRR13808065`	ribo-seq	leaf_V2_stage_riboseq_2
`SRR13808066`	ribo-seq	leaf_booting_stage_riboseq_2

Tomato (`tomato`, SL3)

file_id	assay	description
`SRX27799703`	ATAC-seq	fruit_0DPA_chromatin_accessibility
`SRX27799731`	ATAC-seq	fruit_10DPA_chromatin_accessibility
`SRX27799719`	ATAC-seq	fruit_3DPA_chromatin_accessibility
`SRX27799727`	ATAC-seq	fruit_5DPA_chromatin_accessibility
`SRX27799722`	ATAC-seq	fruit_3DBA_chromatin_accessibility
`SRX27799718`	ATAC-seq	fruit_7DPA_chromatin_accessibility
`SRX27799733`	ATAC-seq	leaf_chromatin_accessibility
`SRX29291448`	RNA-seq	fruit_10DPA_MicroTom_gene_expression
`SRX29291447`	RNA-seq	fruit_10DPA_MicroTom_gene_expression_2
`SRX29291446`	RNA-seq	fruit_10DPA_MicroTom_gene_expression_3
`SRX29291445`	RNA-seq	fruit_15DPA_Wild_LA1781_gene_expression
`SRX29291444`	RNA-seq	fruit_5DPA_MicroTom_gene_expression
`SRX29291443`	RNA-seq	fruit_5DPA_MicroTom_gene_expression_2
`SRX29291442`	RNA-seq	fruit_15DPA_Wild_LA1781_gene_expression_2
`SRX29291441`	RNA-seq	fruit_5DPA_MicroTom_gene_expression_3
`SRX29291440`	RNA-seq	fruit_0DPA_MicroTom_gene_expression
`SRX29291439`	RNA-seq	fruit_0DPA_MicroTom_gene_expression_2
`SRX29291438`	RNA-seq	fruit_0DPA_MicroTom_gene_expression_3
`SRX29291431`	RNA-seq	fruit_15DPA_MicroTom_gene_expression
`SRX29291430`	RNA-seq	fruit_15DPA_MicroTom_gene_expression_2

Cattle (`cattle`, ARS-UCD1.2)

file_id	assay	description
`ERR1464183`	RNA-seq	spleen_gene_expression
`ERR1464180`	RNA-seq	left_lung_lobe_gene_expression
`ERR1464175`	RNA-seq	hypothalamus_gene_expression
`ERR2664213`	RNA-seq	CD8_gene_expression
`ERR1464174`	RNA-seq	frontal_cortex_gene_expression
`SRX9176795`	ATAC-seq	lung_chromatin_accessibility
`ERX2628478`	ATAC-seq	cd4_chromatin_accessibility
`ERX2628481`	ATAC-seq	cd8_chromatin_accessibility
`SRX5649072`	ATAC-seq	rumen_epithelial_cells_chromatin_accessibility
`SRX9176799`	ATAC-seq	skeletal_muscle_chromatin_accessibility
`SRX9176803`	ATAC-seq	spleen_chromatin_accessibility
`SRX7703304`	ATAC-seq	embryo_day_14_elongating_chromatin_accessibility
`ERX5798621`	Histone ChIP-seq	hypothalamus_H3K4Me3
`ERX5798616`	Histone ChIP-seq	frontal_cortex_H3K4Me3
`ERX5798633`	Histone ChIP-seq	semimembranosus_muscle_H3K4Me3
`ERX4795023`	Histone ChIP-seq	liver_H3K27Me3
`ERX5798749`	Histone ChIP-seq	semimembranosus_muscle_H3K4Me1
`ERX4794967`	Histone ChIP-seq	renal_medulla_H3K4Me1
`ERX4795038`	Histone ChIP-seq	mammary_gland_H3K27Ac
`ERX5798687`	Histone ChIP-seq	semimembranosus_muscle_H3K27Ac
`ERX4794981`	Histone ChIP-seq	lung_H3K27Ac
`ERX4795026`	Histone ChIP-seq	liver_H3K4Me1
`ERX4794986`	Histone ChIP-seq	mammary_gland_H3K27Me3
`ERX5798711`	Histone ChIP-seq	semimembranosus_muscle_H3K27Me3
`ERX4795019`	TF ChIP-seq	renal_medulla_CTCF
`ERX4795059`	TF ChIP-seq	kidney_CTCF
`ERX4794984`	TF ChIP-seq	lung_CTCF
`ERX4795088`	TF ChIP-seq	spleen_CTCF
`ERX3800751`	TF ChIP-seq	cerebellum_CTCF
`ERX4795054`	TF ChIP-seq	heart_CTCF

Fission yeast (`fission_yeast`, ASM294v2)

file_id	assay	description
`SRX893731`	ATAC-seq	1m_5min_chromatin_accessibility
`SRX893735`	ATAC-seq	20m_20min_chromatin_accessibility
`SRX893733`	ATAC-seq	20m_5min_chromatin_accessibility
`SRX893734`	ATAC-seq	5m_20min_chromatin_accessibility
`SRX893732`	ATAC-seq	5m_5min_chromatin_accessibility
`ERR1162944`	RNA-seq	grown_with_nitrogen_gene_expression
`ERR1162946`	RNA-seq	grown_without_nitrogen_gene_expression

Malaria parasite (`malaria_parasite`, GCA000002765v3)

file_id	assay	description
`SRR16019126`	RNA-seq	ring_10-15_hpi_gene_expression
`SRR16019133`	RNA-seq	schizont_40-45_hpi_gene_expression
`SRR16019130`	RNA-seq	trophozoite_25-30_hpi_gene_expression
`SRX5494567`	ATAC-seq	stage_10hpi_chromatin_accessibility
`SRX5494566`	ATAC-seq	stage_20hpi_chromatin_accessibility
`SRX5494565`	ATAC-seq	stage_30hpi_chromatin_accessibility
`SRX5494564`	ATAC-seq	stage_40hpi_chromatin_accessibility

Rat (`rat`, mRatBN7)

file_id	assay	description
`SRR594428`	RNA-seq	brain_gene_expression
`SRR594429`	RNA-seq	colon_gene_expression
`SRR594430`	RNA-seq	heart_gene_expression
`SRR594431`	RNA-seq	kidney_gene_expression
`SRR594432`	RNA-seq	liver_gene_expression
`SRR594433`	RNA-seq	lung_gene_expression
`SRR594434`	RNA-seq	skeletal_muscle_gene_expression
`SRR594435`	RNA-seq	spleen_gene_expression
`SRR594436`	RNA-seq	testes_gene_expression
`SRX9339411`	ATAC-seq	liver_chromatin_accessibility
`SRX9339415`	ATAC-seq	primary_motor_cortex_m1_chromatin_accessibility
`SRX9339416`	ATAC-seq	striatum_chromatin_accessibility

Soil amoeba (`soil_amoeba`, dicty_2.7)

file_id	assay	description
`SRR12055126`	RNA-seq	dev_stage_hr00_gene_expression
`SRR12055127`	RNA-seq	dev_stage_hr04_gene_expression
`SRR12055128`	RNA-seq	dev_stage_hr08_gene_expression
`SRR12055129`	RNA-seq	dev_stage_hr12_gene_expression
`SRR12055130`	RNA-seq	dev_stage_hr16_gene_expression
`SRR12055131`	RNA-seq	dev_stage_hr20_gene_expression
`SRR12055132`	RNA-seq	dev_stage_hr24_gene_expression

Yeast (`yeast`, R64)

file_id	assay	description
`SRX893741`	ATAC-seq	0.6_m_nacl_15_minutes_chromatin_accessibility
`SRX893743`	ATAC-seq	0.6_m_nacl_30_minutes_chromatin_accessibility
`SRX893745`	ATAC-seq	0.6_m_nacl_45_minutes_chromatin_accessibility
`SRX893747`	ATAC-seq	0.6_m_nacl_60_minutes_chromatin_accessibility
`SRX893737`	ATAC-seq	chromatin_accessibility
`ERR3772438`	RNA-seq	ethanol_cycle_102min_gene_expression
`ERR3772439`	RNA-seq	ethanol_cycle_132min_gene_expression
`ERR3772440`	RNA-seq	ethanol_cycle_142min_gene_expression
`ERR3772434`	RNA-seq	ethanol_cycle_14min_gene_expression
`ERR3772428`	RNA-seq	ethanol_cycle_162min_gene_expression
`ERR3772436`	RNA-seq	ethanol_cycle_20min_gene_expression
`ERR3772430`	RNA-seq	ethanol_cycle_92min_gene_expression

Changes from `InstaDeepAI/NTv3_benchmark_dataset`

Genome annotation BED files (exon, intron, splice acceptor, start codon) are removed: the benchmark only covers functional tracks.
Chicken is removed.
Cattle now uses the ARS-UCD1.2 assembly (the previous genome.fasta was ARS-UCD2.0) with its benchmark splits, and gains its 30 functional tracks.
New species: fission yeast, malaria parasite, rat, soil amoeba and yeast.
benchmark_metadata.tsv gains a description column.

NTv3 Benchmark Dataset (revised)

Dataset organization

Species

Files

Target scaling used in the benchmark

Download

Tracks

Arabidopsis (arabidopsis, TAIR10)

Human (human, hg38)

Maize (maize, Zm-B73-REFERENCE-NAM-5.0)

Rice (rice, IRGSP-1.0)

Tomato (tomato, SL3)

Cattle (cattle, ARS-UCD1.2)

Fission yeast (fission_yeast, ASM294v2)

Malaria parasite (malaria_parasite, GCA000002765v3)

Rat (rat, mRatBN7)

Soil amoeba (soil_amoeba, dicty_2.7)

Yeast (yeast, R64)

Changes from InstaDeepAI/NTv3_benchmark_dataset