datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
genomes-v4-genome_set-animals-intervals-v5_256_128genomes-v5-genome_set-animals-intervals-v1_255_128
bolinas-dna/genomes-v5-genome_set-animals-intervals-v1_255_128
Animals promoters (v1) sequences — 255 bp DNA windows
for genomic language model pretraining.
Part of the bolinas-dna/genomes-v5 training-dataset family produced by the
snakemake/training_dataset pipeline (commit
8db58254831f). Each repo in the family is one
(genome_set, region-recipe) combination.
Size
68,286,166 sequences across 64 data/train/*.jsonl.zst shards
(reverse complements included). This is… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/genomes-v5-genome_set-animals-intervals-v1_255_128.genomes-v4-genome_set-animals-intervals-v11_256_128genomes-v5-genome_set-animals_order204-intervals-v5_255_128
bolinas-dna/genomes-v5-genome_set-animals_order204-intervals-v5_255_128
204 animals (one per order) CDS (v5) sequences — 255 bp DNA windows
for genomic language model pretraining.
Part of the bolinas-dna/genomes-v5 training-dataset family produced by the
snakemake/training_dataset pipeline (commit
main). Each repo in the family is one
(genome_set, region-recipe) combination.
Size
101,114,252 sequences across 64 data/train/*.jsonl.zst shards
(reverse complements… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/genomes-v5-genome_set-animals_order204-intervals-v5_255_128.genomes-v4-genome_set-animals-intervals-v10_256_128genomes-v4-genome_set-animals-intervals-v12_256_128genomes-v4-genome_set-animals-intervals-v4_512_256genomes-v4-genome_set-animals-intervals-v13_256_128genomes-v4-genome_set-animals-intervals-v14_256_128genomes-v4-genome_set-animals-intervals-v1_256_128zoonomia-v1-v4_ccre_noexon
bolinas-dna/zoonomia-v1-v4_ccre_noexon
A curated enhancer training set for issue
#326 — a de-contaminated
derivation of the v4 ccre_non_promoter arm of
bolinas-dna/zoonomia-v1-v1,
built by the
snakemake/zoonomia_projection_dataset pipeline at commit
6b320c268547.
Provenance
This subset is the v4 ccre_non_promoter arm with every window that overlaps any other functional element (CDS / 3′UTR / ncRNA exon / TSS+5′UTR) removed — i.e. windows whose functional content… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v4_ccre_noexon.genomes-v5-genome_set-animals-intervals-v5_255_128
bolinas-dna/genomes-v5-genome_set-animals-intervals-v5_255_128
Animals CDS (v5) sequences — 255 bp DNA windows
for genomic language model pretraining.
Part of the bolinas-dna/genomes-v5 training-dataset family produced by the
snakemake/training_dataset pipeline (commit
8db58254831f). Each repo in the family is one
(genome_set, region-recipe) combination.
Size
242,334,716 sequences across 64 data/train/*.jsonl.zst shards
(reverse complements included). This is an… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/genomes-v5-genome_set-animals-intervals-v5_255_128.zoonomia-v1-v4_ccre_noexon_enhancer
bolinas-dna/zoonomia-v1-v4_ccre_noexon_enhancer
A curated enhancer training set for issue
#326 — a de-contaminated
derivation of the v4 ccre_non_promoter arm of
bolinas-dna/zoonomia-v1-v1,
built by the
snakemake/zoonomia_projection_dataset pipeline at commit
6b320c268547.
Provenance
This subset is v4_ccre_noexon further restricted to enhancer-dominant windows (dELS+pELS basepair coverage ≥ the other non-PLS cCRE classes), population-matching the val_enhancer… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v4_ccre_noexon_enhancer.zoonomia-v1-v3_cds
bolinas-dna/zoonomia-v1-v3_cds
Per-anchor region-type partition of the cross-mammal training set
bolinas-dna/zoonomia-v1-v1,
restricted to anchors labelled cds by the
snakemake/zoonomia_projection_dataset pipeline
(commit 2ab868a2f1d4).
Region label (cds)
Coding sequence — Ensembl r115 CDS features (get_cds). Highest-priority class: any anchor with overlap on a CDS feature (and union-of-functional fraction ≥ 0.20 across all five labels) is labelled cds, regardless… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v3_cds.genomes-v4-genome_set-animals-intervals-v6_256_128gpn-star-p-uniform-v1-cds
marin-dna/gpn-star-p-uniform-v1-cds
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment.
This draft covers the cds region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
Anchor eligibility uses calibrated entropy from the primate… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/gpn-star-p-uniform-v1-cds.zoonomia-v1-v3_ccre_non_promoter
bolinas-dna/zoonomia-v1-v3_ccre_non_promoter
Per-anchor region-type partition of the cross-mammal training set
bolinas-dna/zoonomia-v1-v1,
restricted to anchors labelled ccre_non_promoter by the
snakemake/zoonomia_projection_dataset pipeline
(commit 2ab868a2f1d4).
Region label (ccre_non_promoter)
ENCODE cCRE V4 non-promoter classes — cre_class != "PLS" (so: dELS, pELS, CA, CA-CTCF, CA-TF, CA-H3K4me3, TF), extended by 500 bp on each side. PLS is excluded because… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v3_ccre_non_promoter.gpn-star-p-uniform-v1-background
marin-dna/gpn-star-p-uniform-v1-background
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment.
This draft covers the background region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
Anchor eligibility uses calibrated entropy from the primate… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/gpn-star-p-uniform-v1-background.phylop-uniform-v1-cds
marin-dna/phylop-uniform-v1-cds
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment.
This draft covers the cds region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
Anchor eligibility uses the pipeline's pinned phyloP conservation filter.
Sequence… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/phylop-uniform-v1-cds.gpn-star-p-uniform-v1-enhancer-arm-a
marin-dna/gpn-star-p-uniform-v1-enhancer-arm-a
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment.
This draft covers the enhancer region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
Anchor eligibility uses calibrated entropy from the primate… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/gpn-star-p-uniform-v1-enhancer-arm-a.functional-cds
marin-dna/functional-cds
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and official version-matched UCSC hg38-to-target liftOver chains.
This draft covers the cds region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
For the 28 non-mammalian targets, the stable ucsc_multiz100way… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/functional-cds.genomes-v4-genome_set-animals-intervals-v8_256_128zoonomia-v1-v1
zoonomia-v1-v1
255 bp human-anchored windows, conservation-filtered (phyloP_447m, proportion_conserved >= 0.20), projected onto 108 family-deduped Zoonomia 447-mammalian assemblies via halLiftover, midpoint-resized to 255 bp, reverse-complement-augmented. Single train split.
Produced by the zoonomia_projection_dataset pipeline in Open-Athena/bolinas-dna — permalinked at the exact code that built this dataset: snakemake/zoonomia_projection_dataset @ 7ff07cd (PR #158).… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v1.genomes-v4-genome_set-animals-intervals-v9_256_128genomes-v4-genome_set-animals-intervals-v15_256_128vertebrate-v1-issue473-fullwindow-cds-random-val
marin-dna/vertebrate-v1-issue473-fullwindow-cds-random-val
CDS full-window vertebrate projection sequences for the issue #473 random
validation control. The source is the immutable issue #417 accepted-sequence
table.
The split uniformly samples 16,384 original-orientation CDS rows
without replacement using seed 42. Sampling occurs before
reverse-complement augmentation. Selected rows are removed from training;
reverse complements are then added only to the remaining training… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/vertebrate-v1-issue473-fullwindow-cds-random-val.genomes-v5-genome_set-animals-intervals-v15_255_128
bolinas-dna/genomes-v5-genome_set-animals-intervals-v15_255_128
Animals downstream-of-CDS (v15) sequences — 255 bp DNA windows
for genomic language model pretraining.
Part of the bolinas-dna/genomes-v5 training-dataset family produced by the
snakemake/training_dataset pipeline (commit
8db58254831f). Each repo in the family is one
(genome_set, region-recipe) combination.
Size
20,501,856 sequences across 64 data/train/*.jsonl.zst shards
(reverse complements… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/genomes-v5-genome_set-animals-intervals-v15_255_128.genomes-v5-genome_set-vertebrates-intervals-v5_255_128
bolinas-dna/genomes-v5-genome_set-vertebrates-intervals-v5_255_128
Vertebrates CDS (v5) sequences — 255 bp DNA windows
for genomic language model pretraining.
Part of the bolinas-dna/genomes-v5 training-dataset family produced by the
snakemake/training_dataset pipeline (commit
8db58254831f). Each repo in the family is one
(genome_set, region-recipe) combination.
Size
172,025,122 sequences across 64 data/train/*.jsonl.zst shards
(reverse complements included). This… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/genomes-v5-genome_set-vertebrates-intervals-v5_255_128.vertebrate-v1-all
marin-dna/vertebrate-v1-all
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment. This
draft covers the all region cohort with all species
scope and preserves source FASTA/2bit letter case.
Anchor eligibility uses the pipeline's pinned phyloP conservation filter.
Sequence case is independent of that filter: lowercase bases preserve source
repeat masking, uppercase bases preserve source non-repeat-masked… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/vertebrate-v1-all.phylop-uniform-v1-enhancer-arm-a
marin-dna/phylop-uniform-v1-enhancer-arm-a
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment.
This draft covers the enhancer region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
Anchor eligibility uses the pipeline's pinned phyloP conservation… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/phylop-uniform-v1-enhancer-arm-a.