BrentLab/yeast_genome_resources

BrentLab Yeast Genome Resources

This Dataset stores resources meant to make data exploration of yeast -omic data, curated by the Brent Lab, easier and more harmonious.
To cite, cite SGD

Usage

You may access just the Dataset metadata like this:

from huggingface_hub import ModelCard

card = ModelCard.load("BrentLab/yeast_genome_resources", repo_type="dataset")

# cast to dict
card_dict = card.data.to_dict()

# Get partition information
card_dict.get("dataset_info").get("partitioning").get("keys")

Output:

[{'name': 'chr',
  'dtype': 'string',
  'levels': 'chrI,chrII,chrVII,chrV,chrIII,chrIV,chrVIII,chrVI,chrX,chrIX,chrXI,chrXIV,chrXII,chrXIII,chrXV,chrXVI,chrM'}]

You can use this information to pull only the partition you're interested in, eg

from huggingface_hub import hf_hub_download

# Download a single partition file and store it in the local cache
local_file = hf_hub_download(
    repo_id="BrentLab/yeast_genome_resources",
    repo_type="dataset",
    filename="features/chr=chrII/part-0.parquet"
)

Dataset Details

Dataset Sources

• Source: SGD S288C Reference Files
  This is derived from S288C_reference_genome_R64-3-1_20210421.tgz

The .bed files are derived from annotation set 5-1 rather than 3-1 and the following loci are not included in the metadata above

"YDL204W-A" "YFR035W-A" "YGR016C-A" "YMR106W-A" "YNL040C-A" "YNL155C-A"

See scripts/ for details on how the tss are extracted from the SGD annotations (verison 5-1)

Dataset Structure

Features/

This is a Parquet dataset where the partitions are based on chr. Each row represents a genomic feature, and the columns are described below:

Field	Description
chr	Chromosome name (e.g., chrI, chrII, ..., chrM) in UCSC format
start	Start coordinate (1-based, inclusive)
end	End coordinate (1-based, inclusive)
strand	Strand: either + or -
type	Feature type — one of: gene, ncRNA_gene, tRNA_gene, snoRNA_gene, transposable_element_gene, pseudogene, telomerase_RNA_gene, snRNA_gene, rRNA_gene, blocked_reading_frame
locus_tag	Systematic gene identifier
symbol	Common name of the feature
alias	Alternate names (usually similar to symbol)
source	Origin or authority of the annotation
note	Description provided in the original GFF record

Dataset Author and Contact: Chase Mateusiak @cmatKhan