Datasets:

HuggingFaceBio
/

random-promoter-dream-2022

license: cc-by-4.0
task_categories:
  - text-regression
language:
  - en
tags:
  - biology
  - dna
  - genomics
  - promoter
  - gene-expression
  - carbon

Random Promoter DREAM Challenge 2022

This dataset repackages the processed Random Promoter DREAM Challenge 2022 files from Zenodo record 10633252 for use with datasets.

The task is sequence-to-expression regression on synthetic yeast promoter sequences. The canonical supervised config contains random promoter training examples, validation examples, and labeled designed test promoters.

Configs

supervised: train, validation, and test splits with promoter sequences and measured activity.
challenge_test_sequences: unlabeled test sequences for submission-style prediction workflows.
test_subset_membership: normalized IDs from test_subset_ids.tar.gz.
public_leaderboard_ids: normalized IDs from public_leaderboard_ids.tar.gz.

Schema

supervised:

sequence: DNA sequence.
activity: measured promoter activity.
sequence_length: sequence length in base pairs.
source_file: source filename.
row_id: zero-based row index within the source split.

ID metadata configs:

subset: subset name inferred from the archive member.
item_id: raw ID token from the source line.
row_id: integer row ID when item_id is numeric; otherwise -1.
source_member: archive member path.
line_number: line number within the member.
raw_line: unmodified stripped source line.

Usage

from datasets import load_dataset

ds = load_dataset("HuggingFaceBio/random-promoter-dream-2022", "supervised")
train = ds["train"]
validation = ds["validation"]
test = ds["test"]

subsets = load_dataset("HuggingFaceBio/random-promoter-dream-2022", "test_subset_membership", split="train")

Source

Source: Random Promoter DREAM Challenge 2022, Zenodo DOI 10.5281/zenodo.10633252.

The source record is licensed CC BY 4.0. Cite the original DREAM Challenge data and paper when using this dataset.

Reproduction

This dataset repo includes create_dataset.py, the script used to download, convert, and upload the configs.