Add the dataset card, all-isoform references and whole test genomes

README.md

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+---
+language:
+  - en
+pretty_name: "NTv3 annotation dataset - Genomes & reference gene annotations"
+tags:
+  - 🧬 genomics
+  - 🏷️ gene annotation
+  - 🎯 benchmark
+  - ⚡ fine-tuning
+  - 🔬 bioinformatics
+task_categories:
+  - other
+size_categories:
+  - n<1K
+license: cc-by-nc-4.0
+---
+
+# NTv3 Annotation Dataset
+
+Genomes and reference gene annotations behind the NTv3 gene-annotation models
+([`NTv3_annot_mammals`](https://huggingface.co/InstaDeepAI/NTv3_annot_mammals),
+[`NTv3_annot_plants`](https://huggingface.co/InstaDeepAI/NTv3_annot_plants),
+[`NTv3_annot_insects`](https://huggingface.co/InstaDeepAI/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_revised`](https://huggingface.co/spaces/InstaDeepAI/ntv3_revised) 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
+
+```python
+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.

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