InstaDeepAI/NTv3_annot_dataset

NTv3 Annotation Dataset

Genomes and reference gene annotations behind the NTv3 gene-annotation models (NTv3_annot_mammals, NTv3_annot_plants, NTv3_annot_insects). It holds two things:

• The benchmark: the 17 test species held out from training (2 mammals, 5 plants, 10 insects). Each species comes with its complete soft-masked genome, the reference annotation the benchmark scores against, and the reference's every annotated isoform. The models' own predictions on these genomes are in each model repository's annot_results/ folder.
• The plant tutorial data: training and validation genomes with per-base labels, used by the genome-annotation notebooks of the ntv3 Space (03a training, 03b decoding, 03c evaluation).

Dataset organization

InstaDeepAI/NTv3_annot_dataset/
├── <clade>/test_species/<assembly>/     # clade = mammals, plants or insects
│   ├── genome.fa.gz                     # soft-masked genome, bgzipped
│   ├── genome.fa.gz.fai                 # samtools faidx index
│   ├── genome.fa.gz.gzi                 # bgzip index
│   ├── reference_longest_isoform.gff3.gz
│   ├── reference_all_isoforms.gff3.gz
│   └── pseudogenes.bed
└── plants/
    ├── metadata.tsv                     # one row per tutorial species
    ├── class_counts.json
    ├── class_weights.json
    ├── train_species/<assembly>/        # genome.fa.gz(.fai, .gzi), labels.bed.gz
    ├── val_species/<assembly>/          # same as test species, plus labels.bed.gz,
    │                                    #   without reference_all_isoforms.gff3.gz
    └── test_species/<assembly>/         # Medicago and Mimulus also carry labels.bed.gz;
                                         #   Medicago carries demo_log_probs/

Folders are named by assembly, as in the model repositories' annot_results/ files.

Files

• genome.fa.gz: the soft-masked genome (repeats in lowercase), bgzipped, one record per sequence, record names cut to the sequence ID. For test species it is the complete assembly, every contig, with the sequence names of the reference annotation. Tutorial training and validation genomes keep only the contigs of at least 131,072 bp, the tutorial's training window.
• reference_longest_isoform.gff3.gz: the reference the benchmark scores against. Protein-coding genes only, one transcript per gene (the one with the longest CDS), gene, mRNA and CDS rows, ID and Parent attributes only. 1-based closed coordinates (GFF3).
• reference_all_isoforms.gff3.gz (test species): the same genes, with every transcript the source annotation release gives them, in the same format. A prediction that matches any transcript of a gene counts under the any-isoform rule. When the source release does not carry a reference transcript's exact CDS, that transcript is kept as well, so the file is a strict superset of the longest-isoform reference: 171 genes whose IDs were assigned when the longest isoform was extracted (agat-gene-*: 151 immune receptor gene segments in cow and whale, 15 chloroplast genes, 5 insect genes) and one transcript in cow (PEG10, ID suffixed .longest_isoform).
• pseudogenes.bed: pseudogene regions of the source annotation that do not overlap a reference CDS. Predicted genes there are ignored when scoring. BED, 0-based half-open.
• labels.bed.gz (tutorial species): the per-base training labels, one of 15 classes (intergenic, intron_p0-2, CDS_p0-2, splice_donor_p0-2, splice_acceptor_p0-2, start_codon, stop_codon), as BED runs per strand (chrom, start, end, class, ., strand), 0-based half-open.
• plants/metadata.tsv: the tutorial species, their role (train, validation, test), tier (the tutorial's presets train on tiers 1-2), source, accession and the chromosome the tutorial evaluates on (eval_chromosomes).
• plants/class_counts.json: per-species base counts of each class. Notebook 03a derives its loss weights from them, for the genomes it trains on.
• plants/class_weights.json: those weights precomputed over all the training genomes (mean inverse class frequency).
• demo_log_probs/ (Medicago): precomputed per-base log-probabilities of NTv3_annot_plants over NC_053042.1:11,010,048-12,582,912, decoded in notebook 03b; meta.json records the model, code revision, windows and hardware.

Scores are gene- and CDS-level F1: a predicted gene counts only if its whole CDS structure matches exactly, predicted genes with less than 201 nt of CDS are ignored, and so are those in pseudogenes.bed. Notebook 03c implements the evaluation.

Test species

Clade	Folder	Species	Contigs	Genes	Transcripts	Genome	Reference annotation
mammals	GCF_002263795.3_ARS-UCD2.0	Bos taurus (cow)	1,958	21,577	49,639	NCBI RefSeq	NCBI RefSeq GCF_002263795.3-RS_2024_12
mammals	GCF_002288925.2_ASM228892v3	Delphinapterus leucas (beluga whale)	5,905	18,389	40,864	NCBI RefSeq	NCBI RefSeq Annotation Release 101
plants	GCF_000005505.3_Brachypodium_distachyon_v3.0	Brachypodium distachyon	11	25,477	32,269	NCBI RefSeq	NCBI RefSeq Annotation Release 103
plants	EcalifornicavarOrangeKingHAP1v1.1	Eschscholzia californica 'Orange King' HAP1	6	29,562	42,970	Phytozome 828	Phytozome v1.1
plants	FmultifloravarABG20040013HAP1v1.1	Freycinetia multiflora ABG20040013 HAP1	30	28,264	38,805	Phytozome 868	Phytozome v1.1
plants	GCF_003473485.1_MtrunA17r5.0-ANR	Medicago truncatula	42	31,794	37,660	NCBI RefSeq	NCBI RefSeq GCF_003473485.1-RS_2025_04
plants	MguttatusvarIM62v3.1	Mimulus guttatus IM62	23	25,096	31,078	Phytozome 797	Phytozome v3.1
insects	GCF_030269925.1_ASM3026992v2	Bombyx mori	30	13,251	22,941	NCBI RefSeq	NCBI RefSeq GCF_030269925.1-RS_2024_01
insects	GCF_021464435.1_ULB_Chis1_1.0	Cataglyphis hispanica	453	10,380	17,463	NCBI RefSeq	NCBI RefSeq Annotation Release 100
insects	GCF_905220415.1_ilColCroc2.1	Colias croceus	32	13,364	18,775	NCBI RefSeq	NCBI RefSeq Annotation Release 100
insects	GCF_018135715.1_MEX_DaPlex	Danaus plexippus	66	12,669	19,058	NCBI RefSeq	NCBI RefSeq GCF_018135715.1-RS_2023_11
insects	GCF_905404315.1_ilLepSina1.1	Leptidea sinapis	49	12,276	19,563	NCBI RefSeq	NCBI RefSeq Annotation Release 100
insects	GCF_905147045.1_ilAglIoxx1.1	Nymphalis io (syn. Aglais io)	41	12,024	18,680	NCBI RefSeq	NCBI RefSeq Annotation Release 100
insects	GCF_907164935.1_iOsmBic2.1	Osmia bicornis	441	11,262	18,822	NCBI RefSeq	NCBI RefSeq Annotation Release 101
insects	GCF_031307605.1_icTriCast1.1	Tribolium castaneum	149	11,953	19,088	NCBI RefSeq	NCBI RefSeq GCF_031307605.1-RS_2024_04
insects	GCF_905220365.1_ilVanCard2.1	Vanessa cardui	36	13,070	17,975	NCBI RefSeq	NCBI RefSeq Annotation Release 100
insects	GCF_012273895.1_Zerene_cesonia_1.1	Zerene cesonia	275	11,791	15,989	NCBI RefSeq	NCBI RefSeq Annotation Release 100

Genes is the number of reference genes; Transcripts, the coding transcripts in reference_all_isoforms.gff3.gz. NCBI genomes are the _genomic.fna.gz of the assembly; the Phytozome genomes are its softmasked FASTA (Freycinetia: the 30 scaffolds of Phytozome 868 concatenated).

Plant tutorial species

Role	Folder	Species	Source
train (tier 1)	TAIR10	Arabidopsis thaliana	Ensembl Plants (Araport11 genes)
train (tier 1)	GCF_000004075.3_Cucumber_9930_V3	Cucumis sativus	NCBI RefSeq
train (tier 1)	GCF_022201045.2_DVS_A1.0	Citrus sinensis	NCBI RefSeq
train (tier 1)	GCF_019578655.1_ASM1957865v1	Ricinus communis	NCBI RefSeq
train (tier 1)	GCF_020921035.1_ASM2092103v1	Rhodamnia argentea	NCBI RefSeq
train (tier 1)	GCF_005286985.2_Setaria_viridis_v4.0	Setaria viridis	NCBI RefSeq
train (tier 1)	GCF_016808095.1_ASM1680809v1	Vigna angularis	NCBI RefSeq
train (tier 1)	GCF_030704535.1_ASM3070453v1	Vitis vinifera	NCBI RefSeq
train (tier 2)	GCF_031755915.1_ASM3175591v1	Ziziphus jujuba	NCBI RefSeq
train (tier 2)	GCF_018687715.1_C.illinoinensisPawnee_v1	Carya illinoinensis	NCBI RefSeq
train (tier 2)	GCF_036884655.1_Cavendish_Baxijiao_AAA	Musa acuminata	NCBI RefSeq
train (tier 2)	GCF_958298935.1_lpPhrAust1.1	Phragmites australis	NCBI RefSeq
train (tier 2)	IRGSP-1.0	Oryza sativa	Ensembl Plants genome, NCBI RefSeq genes
validation	GCF_000002775.5_P.trichocarpa_v4.1	Populus trichocarpa	NCBI RefSeq
validation	Tlatifoliav1.1	Typha latifolia	JGI (GenBank copy, GCA_059706395.1)
test	GCF_003473485.1_MtrunA17r5.0-ANR	Medicago truncatula	see the test species table
test	MguttatusvarIM62v3.1	Mimulus guttatus IM62	see the test species table

plants/metadata.tsv also lists tier 3-4 species; their files are not in this dataset.

Download

from huggingface_hub import hf_hub_download, snapshot_download

# One file
path = hf_hub_download(
    "InstaDeepAI/NTv3_annot_dataset",
    "mammals/test_species/GCF_002288925.2_ASM228892v3/reference_longest_isoform.gff3.gz",
    repo_type="dataset",
)

# One species
local_dir = snapshot_download(
    "InstaDeepAI/NTv3_annot_dataset",
    repo_type="dataset",
    allow_patterns="plants/test_species/GCF_003473485.1_MtrunA17r5.0-ANR/*",
)

Sources and licence

The files we derived (labels, class statistics, log-probabilities) are released under CC BY-NC 4.0. Genomes and reference annotations are redistributed from NCBI RefSeq, Ensembl Plants and JGI Phytozome under their own terms; please cite the original assemblies and annotations. The three Phytozome genomes are listed as unrestricted:

• Mimulus guttatus IM62 (assembly v3.0, annotation v3.1): Lovell et al., Molecular Ecology Resources (2025), https://doi.org/10.1111/1755-0998.70012
• Eschscholzia californica 'Orange King' HAP1 v1.1: Rössner et al., The Plant Cell (2026), https://doi.org/10.1093/plcell/koag039
• Freycinetia multiflora ABG20040013 HAP1 (assembly v1.0, annotation v1.1): JGI Open Green Genomes, https://doi.org/10.25585/1488189

Citation

Citation to be added on publication.